research communications
Crystal structures of Z–Gly–Aib–O−·0.5Ca2+·H2O and Z–Gly–Aib–OH
aIMBB-FORTH, 70013 Heraklion, Greece, and bDepartment of Food Sciences, Interdisciplinary Research Center, Justus-Liebig-University of Giessen, 35392 Giessen, Germany
*Correspondence e-mail: petratos@imbb.forth.gr
Both deprotonated and neutral achiral title dipeptides assume similar structures of two conformations, which are related by a unit-cell inversion centre. Two molecules of both conformations of the metal-free neutral dipeptide are linked by two hydrogen bonds, while two molecules of both conformations of the ionized form coordinate a calcium ion in calcium(II) bis[2-(2-{[(benzyloxy)carbonyl]amino}acetamido)-2-methylpropanoate] monohydrate, 0.5Ca2+·C14H17N2O5−·0.5H2O, which lies on an inversion centre and forms a distorted octahedral complex with the metal ion. These CaII complexes are connected in the crystal via hydrogen bonds in the b- and c-axis directions, whereas in the a-axis direction, they stack via apolar contacts. In the metal-free crystal, namely 2-(2-{[(benzyloxy)carbonyl]amino}acetamido)-2-methylpropanoic acid, C14H18N2O5, molecules are hydrogen bonded in the a- and c-axis directions, and stack in the b–axis direction via apolar contacts.
1. Chemical context
The presence of Gly and Aib (α-aminoisobutyric acid) combines a residue with the greatest conformational flexibility (Gly) with a severely restricted residue (Aib) because of the second methyl group attached to the Cα atom. The space available for Aib comprises the left-handed and right-handed helical region of the Ramachandran plot. Because of the absent side-chain atoms, Gly can adopt almost all conformations in contrast to all other residues. This makes Gly a conserved residue in and proteins because a mutation of Gly could change the flexibility necessary for function or cause significant alteration of the secondary structure. Gly is incorporated in about half of all known peptaibol sequences (Stoppacher et al., 2013) and frequently as a –Aib–Gly– dipeptide or as a –Aib–Gly–Aib– tripeptide unit. composed of Aib and Gly only show an enormous structural flexibility (Gessmann et al., 1991; Gessmann, Brückner, Aivaliotis et al., 2015; Gessmann, Brückner & Petratos, 2015) and therefore normally normally do not yield suitable sized crystals for structure analysis with X-rays.
2. Structural commentary
In the I (Z–Gly–Aib-O−·0.5Ca2+·H2O) all expected non H-atoms in both dipeptides were readily visible in the first electron-density map as the highest peaks. In addition, a heavy atom was detected, which at a later stage was identified as calcium by energy-dispersive (EDS), together with a water oxygen atom.
ofThe backbone conformation of both ). Gly is in the semi-extended conformation of both handednesses with torsion angles φ = ∓62.2 (2)°, ψ = ±153.37 (18)° in I and φ = ∓59.37 (14)°, ψ = ±153.66 (10)° in II (Z–Gly–Aib–OH). Aib adopts φ = ±54.8 (3) and ±55.86 (14)° in I and II, respectively, while the values of ψ with both O atoms are ∓154.7 (2) or ±29.7 (3)° in I and ∓145.5 (1) or ±41.0 (1)° in II and therefore lies in the helical region of the Ramachandran plot. The Z-protection groups (benzyloxycarbonyl) adopt different conformations in I and II (Fig. 2). The r.m.s. deviation for the non-hydrogen atoms of Gly and Aib is 0.2 Å, whereby the most distant carbon atoms of the Z protection group of the two are 4.75 Å apart in the superposition of the non-hydrogen atoms of the amino acid residues.
is very similar (Fig. 1The similar backbone conformation is also visible in Fig. 2. Structure I crystallized with a water molecule and a half calcium ion (lying on a special position) per peptide molecule while II, which crystallized without any solvent molecules, forms two direct hydrogen bonds between two inversion-related molecules. In I the Ca2+ ion is coordinated by the carbonyl group of Z and the deprotonated carboxylate group of Aib2. It is worth noting that in both crystal structures the same oxygen atoms participate in the hydrogen bonding and coordination interactions (Fig. 2). One dipeptide molecule and its inverted mate provide four of the six ligand atoms for the calcium ion. The remaining two ligands are two water molecules, which are also related via the inversion centres. The metal coordination parameters are listed in Table 1. As the calcium ion sits on the inversion centre, the values of the fifteen angles between the ligands are reduced to seven values, each one occurring twice and the 180° angle between the metal ion and inverted atoms occurs three times.
3. Supramolecular features
The crystal packing is quite different in I and II. In the of I, there are four hydrogen bonds between symmetry-related molecules (Table 2). The first hydrogen bond connects the NH group of Gly to the carbonyl group of a Gly residue, which belongs to a symmetry-related molecule, via a screw axis. In Fig. 3a the green and yellow molecules are hydrogen bonded in a zigzag manner down the b axis and the blue and red symmetry-related ones in zigzag manner along the b axis. The second intermolecular hydrogen bond is formed between the NH group of Aib and the carbonyl group of Aib of a y-translated (+1 or −1) molecule, shown as pairs of the same color in Fig. 3a. The same carbonyl group accepts the hydrogen bond from the water molecule. As this water molecule also coordinates the calcium ion, which is bonded to the translated and inverted molecules, multiple bonded molecule layers are formed in the bc plane. These single molecule layers stack together via apolar contacts between the Z protection groups and the Aib side chains, along the a-axis direction (Fig. 4a). The shortest distance between two symmetry-related rings is 3.54 Å and 3.91 Å between the Aib side chain and a symmetry-related ring. The staggering angles between the Z rings of successive sheets are 119.9° while the distance between the centre of the rings is 4.79 Å. Finally, in one layer the rings of the Z protection groups are staggered parallel with a distance of 5.57 Å, which is equal to the length of the b axis.
In the II, one molecule (the left green molecule in Fig. 3b) is hydrogen bonded to four other molecules. The carbonyl group of Z and the C-terminal OH group of Aib are hydrogen bonded to the same molecule (Fig. 3b) and to the left green molecule. The NH group of Gly is hydrogen bonded to the carbonyl group of Gly1 of the right green molecule in Fig. 3b and Table 3. From the latter molecule the NH-group of Gly1 is a hydrogen-bond donor to the carbonyl group of Gly1 of the central molecule. The same carbonyl group of Gly1 is hydrogen bonded to the NH group of Aib2 of the left red molecule, while the NH group of the central molecule is hydrogen bonded to the carbonyl group of Aib2 of the right red molecule in Fig. 3b. From the same NH group of Aib2 there is a hydrogen-bonding distance of 3.31 Å to the carbonyl group of the same red molecule. The N—H⋯O distance is 2.95 Å and the N—H⋯O angle is 107°, which are too long and too acute for hydrogen bonding; thus this carbonyl oxygen, which is the only potential hydrogen-bond former, remains non-bonded. Fig. 4b shows all eight symmetry-related molecules of the in different colors, zooming out from the central yellow molecule in Fig. 3b. Layers of hydrogen-bonded molecules are formed in the ac plane, which stack together with the next layers along the b axis via apolar contacts. The rings of the Z groups interact between the layers through π–π stacking with an angle 120.1° and a distance between the centres of the rings of 5.73 Å. The shortest van der Waals distance between two layers is 3.86 Å, measured between two ring atoms of the Z protection groups. The staggering angles between the Z rings inside a sheet are 111.0° and the distance between the centres of the rings is 5.31 Å.
of4. Database survey
The t-butyloxycarbonyl–Gly–Aib–OH has been determined [CSD (Groom et al., 2016) refcode CALFEA; Smith et al., 1981]. The dipeptide assumes a different structure to the ones reported here. The N-terminal protection group points in opposite directions compared to the benzyloxycarbonyl (Z) of the present work. In addition, the of an Aib containing peptide complexed with metal ions has also been determined, namely H–Aib–Gly–OH complexed with copper(II) (CSD refcode MUYNID; Tiliakos et al., 2003). In this structure, one peptide takes part in the coordination of three copper ions and a metal ion is bonded to three This coordination is quite different from the one we have observed in the present work, where two peptide anions coordinate one calcium ion.
of5. Synthesis and crystallization
The dipeptide Z–Gly–Aib–OtBu (OtBu, tert-butoxy) was synthesized in DMF (dimethylformamide) from Z–Gly–OH (purchased from Bachem) and H–Aib–OtBu using HOBt and DCC (N,N′-dicyclohexylcarbodiimide) as coupling reagents. Z–Gly–Aib–OH was obtained from Z–Gly–Aib–OtBu with removal of the tert-butyl-protecting group by disolving in DCM (dichloromethane) and by adding TFA (trifluoro-acetic acid). The were crystallized by slow evaporation from a methanol/water mixture (v:v = 50:50). Crystals of I and II were selected from different crystallization batches. In one crystallization batch, a small amount of calcium salt was present in the solvent, yielding the peptide–metal complex.
6. Measurement and refinement
Both crystals measured have a tiny third dimension. They were mounted on cryoloops without cryoprotectant and were kept in place with a minimal amount of vacuum grease and measured at 100 K. Photographs of the crystals are provided in Fig. S1 of the supporting information.
Diffraction data for the calcium-bound peptide (I) were collected on the microfocus beamline I24 (Evans et al., 2011) of Diamond Light Source in Didcot, England, using a Pilatus3 6M detector (Dectris Ltd, Baden, Switzerland). A dataset of 1800 images covering 360° of rotation was collected in the resolution range 30.0–0.67 Å. 28517 reflections were recorded in total. Of these observed reflections, 4976 were unique. The data were integrated and scaled using the software package XDS (Kabsch, 2010). The initial P21/n was changed to the conventional P21/c with the CCP4 programme suite (Winn et al., 2011).
One single plate of the neutral peptide (II) was used for data collection at our in-house diffractometer and data were integrated and scaled with the Bruker software (Bruker, 2008). Crystal data, data collection and structure details for both crystals are summarized in Table 4.
|
All non-hydrogen atoms and one water oxygen in I were detected in the solutions as highest peaks. The highest peak in I (583:220 to the second highest peak in relative units) in a special position was interpreted from this height as a metal ion. The electron density of the metal ion pointed to more than double the number of electrons as oxygen and was assumed to be calcium. Additional supporting evidence came from the octahedral arrangement of six oxygen atoms around the metal. The central metal ion was unequivocally identified as calcium via Energy-dispersive (EDS, Jeol Scanning Microscope 7000 F) by the occurrence of the characteristic peaks at 0.3 (L), 3.7 (Kα) and 4.0 (Kβ) keV. The spectrum is shown in the supporting information section (Fig. S2).
Supporting information
https://doi.org/10.1107/S2056989018010745/ex2009sup1.cif
contains datablocks I, II. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989018010745/ex2009Isup2.hkl
Structure factors: contains datablock II. DOI: https://doi.org/10.1107/S2056989018010745/ex2009IIsup3.hkl
Fig. S1 The crystals used for data collection. Fig. S2 Energy-dispersive X-ray https://doi.org/10.1107/S2056989018010745/ex2009sup4.pdf
DOI:Data collection: PROTEUM2 (Bruker, 2008) for (II). Cell
XDS (Kabsch, 2010) for (I); SAINT (Bruker, 2008) for (II). Data reduction: XDS (Kabsch, 2010) for (I); SAINT (Bruker, 2008) for (II). For both structures, program(s) used to solve structure: SHELXS86 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2014 (Sheldrick, 2015); molecular graphics: COOT (Emsley et al., 2010), SwissPDBViewer (Guex & Peitsch, 1997). Software used to prepare material for publication: CHEMDRAW (Mills, 2006), ORTEPIII (Burnett & Johnson, (1996), ORTEP-3 for Windows (Farrugia, 2012), POVRAY (Persistence of Vision, 2004), pyMOL (DeLano, 2002) for (I); publCIF (Westrip, 2010) for (II).0.5Ca2+·C14H17N2O5−·0.5H2O | F(000) = 700 |
Mr = 331.35 | Dx = 1.384 Mg m−3 |
Monoclinic, P21/c | Synchrotron radiation, λ = 0.59038 Å |
a = 14.996 (3) Å | Cell parameters from 4716 reflections |
b = 5.5740 (11) Å | θ = 0.7–30° |
c = 20.607 (4) Å | µ = 0.14 mm−1 |
β = 112.55 (3)° | T = 100 K |
V = 1590.8 (6) Å3 | Brick, colourless |
Z = 4 | 0.18 × 0.06 × 0.03 mm |
Pilatus3 6M detector on beamline I24 of Diamond Light Source diffractometer | Rint = 0.128 |
φ–scans | θmax = 26.3°, θmin = 1.2° |
28071 measured reflections | h = −19→19 |
4716 independent reflections | k = −7→7 |
3941 reflections with I > 2σ(I) | l = −29→29 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.078 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.214 | w = 1/[σ2(Fo2) + (0.1201P)2 + 1.1073P] where P = (Fo2 + 2Fc2)/3 |
S = 1.06 | (Δ/σ)max < 0.001 |
4716 reflections | Δρmax = 1.27 e Å−3 |
279 parameters | Δρmin = −0.56 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
C1 | −0.31673 (15) | −0.0754 (5) | 0.26150 (12) | 0.0259 (5) | |
C2 | −0.33650 (17) | 0.1220 (4) | 0.21663 (15) | 0.0312 (5) | |
H2 | −0.285 (2) | 0.245 (6) | 0.2275 (17) | 0.030 (8)* | |
C3 | −0.42513 (18) | 0.1428 (4) | 0.16126 (15) | 0.0310 (5) | |
H3 | −0.435 (2) | 0.268 (6) | 0.1291 (17) | 0.026 (7)* | |
C4 | −0.49525 (17) | −0.0319 (5) | 0.15046 (14) | 0.0291 (5) | |
H4 | −0.558 (2) | −0.007 (6) | 0.1123 (19) | 0.032 (8)* | |
C5 | −0.47630 (16) | −0.2259 (5) | 0.19555 (14) | 0.0294 (5) | |
H5 | −0.527 (2) | −0.367 (6) | 0.1923 (18) | 0.033 (8)* | |
C6 | −0.38720 (16) | −0.2489 (5) | 0.25022 (13) | 0.0276 (5) | |
H6 | −0.373 (3) | −0.377 (8) | 0.283 (2) | 0.049 (11)* | |
C7 | −0.21987 (17) | −0.1049 (5) | 0.31939 (13) | 0.0315 (5) | |
H71 | −0.212 (2) | −0.252 (6) | 0.3567 (19) | 0.036 (8)* | |
H72 | −0.188 (3) | 0.053 (7) | 0.343 (2) | 0.039 (9)* | |
O1 | −0.15523 (11) | −0.1822 (3) | 0.28613 (8) | 0.0257 (4) | |
C | −0.06325 (14) | −0.2165 (4) | 0.32957 (10) | 0.0191 (4) | |
O | −0.03479 (11) | −0.1969 (3) | 0.39390 (8) | 0.0225 (3) | |
N_1 | −0.00723 (12) | −0.2754 (3) | 0.29610 (9) | 0.0172 (3) | |
H_1 | −0.033 (2) | −0.300 (6) | 0.2494 (18) | 0.027 (7)* | |
CA_1 | 0.09504 (14) | −0.3025 (4) | 0.33509 (11) | 0.0182 (4) | |
HA1_1 | 0.1043 (18) | −0.429 (5) | 0.3668 (15) | 0.014 (6)* | |
HA2_1 | 0.125 (2) | −0.342 (6) | 0.3040 (17) | 0.025 (7)* | |
C_1 | 0.14182 (13) | −0.0694 (3) | 0.37032 (10) | 0.0157 (4) | |
O_1 | 0.10901 (11) | 0.1280 (3) | 0.34679 (8) | 0.0207 (3) | |
N_2 | 0.22149 (12) | −0.0984 (3) | 0.42780 (9) | 0.0179 (3) | |
H_2 | 0.229 (3) | −0.223 (8) | 0.440 (2) | 0.043 (10)* | |
CA_2 | 0.27454 (14) | 0.1042 (4) | 0.47072 (11) | 0.0197 (4) | |
CB_2 | 0.34920 (18) | −0.0022 (4) | 0.53830 (14) | 0.0303 (6) | |
HB1_2 | 0.388 (2) | −0.101 (5) | 0.5219 (16) | 0.021 (7)* | |
HB2_2 | 0.316 (2) | −0.089 (5) | 0.5596 (15) | 0.018 (6)* | |
HB3_2 | 0.385 (3) | 0.117 (8) | 0.571 (2) | 0.055 (11)* | |
CG_2 | 0.32397 (17) | 0.2482 (4) | 0.43140 (14) | 0.0268 (5) | |
HG1_2 | 0.366 (2) | 0.152 (6) | 0.4210 (17) | 0.027 (7)* | |
HG2_2 | 0.283 (2) | 0.306 (6) | 0.3910 (18) | 0.030 (8)* | |
HG3_2 | 0.361 (3) | 0.369 (7) | 0.463 (2) | 0.042 (9)* | |
C_2 | 0.20651 (14) | 0.2604 (4) | 0.49373 (10) | 0.0184 (4) | |
O1_2 | 0.22838 (12) | 0.4764 (3) | 0.50765 (9) | 0.0242 (3) | |
O2_2 | 0.13732 (12) | 0.1601 (3) | 0.50138 (9) | 0.0259 (4) | |
Ca_3 | 0.0000 | 0.0000 | 0.5000 | 0.01693 (17) | |
O_4 | 0.09395 (13) | −0.3401 (3) | 0.55420 (9) | 0.0267 (4) | |
H1_4 | 0.148 (4) | −0.398 (10) | 0.541 (3) | 0.079 (15)* | |
H2_4 | 0.071 (4) | −0.503 (10) | 0.570 (3) | 0.095* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0171 (9) | 0.0340 (12) | 0.0251 (10) | 0.0014 (8) | 0.0064 (8) | −0.0075 (9) |
C2 | 0.0234 (10) | 0.0269 (11) | 0.0442 (15) | −0.0030 (8) | 0.0140 (10) | −0.0072 (10) |
C3 | 0.0266 (11) | 0.0263 (11) | 0.0388 (13) | 0.0048 (8) | 0.0111 (10) | 0.0031 (10) |
C4 | 0.0221 (10) | 0.0285 (11) | 0.0311 (12) | 0.0046 (8) | 0.0041 (9) | −0.0030 (9) |
C5 | 0.0203 (10) | 0.0299 (11) | 0.0340 (12) | −0.0023 (8) | 0.0059 (9) | −0.0061 (9) |
C6 | 0.0224 (10) | 0.0313 (12) | 0.0267 (11) | 0.0013 (8) | 0.0067 (9) | −0.0006 (9) |
C7 | 0.0197 (10) | 0.0482 (15) | 0.0251 (11) | 0.0010 (9) | 0.0070 (9) | −0.0115 (10) |
O1 | 0.0161 (7) | 0.0405 (9) | 0.0164 (7) | 0.0025 (6) | 0.0018 (6) | −0.0046 (6) |
C | 0.0173 (9) | 0.0199 (9) | 0.0154 (8) | −0.0030 (6) | 0.0010 (7) | −0.0015 (7) |
O | 0.0214 (7) | 0.0287 (8) | 0.0137 (7) | −0.0026 (5) | 0.0026 (5) | −0.0029 (6) |
N_1 | 0.0151 (7) | 0.0202 (8) | 0.0099 (7) | −0.0005 (5) | −0.0021 (6) | −0.0024 (6) |
CA_1 | 0.0155 (8) | 0.0174 (9) | 0.0160 (8) | 0.0001 (6) | −0.0003 (7) | −0.0048 (7) |
C_1 | 0.0171 (8) | 0.0152 (8) | 0.0112 (7) | −0.0010 (6) | 0.0016 (6) | −0.0017 (6) |
O_1 | 0.0245 (7) | 0.0154 (7) | 0.0137 (6) | 0.0009 (5) | −0.0022 (5) | 0.0020 (5) |
N_2 | 0.0178 (7) | 0.0106 (7) | 0.0175 (8) | −0.0007 (5) | −0.0018 (6) | 0.0010 (6) |
CA_2 | 0.0169 (8) | 0.0154 (8) | 0.0188 (9) | −0.0015 (6) | −0.0019 (7) | 0.0005 (7) |
CB_2 | 0.0233 (11) | 0.0206 (10) | 0.0292 (12) | −0.0004 (7) | −0.0097 (9) | 0.0016 (8) |
CG_2 | 0.0231 (10) | 0.0229 (10) | 0.0349 (12) | −0.0037 (8) | 0.0118 (9) | −0.0022 (9) |
C_2 | 0.0198 (9) | 0.0178 (8) | 0.0116 (8) | −0.0025 (6) | −0.0006 (7) | 0.0020 (6) |
O1_2 | 0.0279 (8) | 0.0148 (7) | 0.0284 (8) | −0.0012 (5) | 0.0090 (7) | −0.0002 (6) |
O2_2 | 0.0265 (8) | 0.0286 (8) | 0.0240 (8) | −0.0100 (6) | 0.0113 (6) | −0.0071 (6) |
Ca_3 | 0.0189 (3) | 0.0166 (3) | 0.0123 (3) | −0.00324 (17) | 0.0026 (2) | −0.00157 (17) |
O_4 | 0.0304 (8) | 0.0194 (7) | 0.0290 (8) | 0.0002 (6) | 0.0101 (7) | 0.0000 (6) |
C1—C6 | 1.385 (3) | CA_1—HA2_1 | 0.94 (3) |
C1—C2 | 1.394 (4) | C_1—O_1 | 1.227 (2) |
C1—C7 | 1.494 (3) | C_1—N_2 | 1.331 (2) |
C2—C3 | 1.385 (4) | N_2—CA_2 | 1.467 (3) |
C2—H2 | 0.99 (3) | N_2—H_2 | 0.73 (4) |
C3—C4 | 1.387 (4) | CA_2—CG_2 | 1.520 (3) |
C3—H3 | 0.94 (3) | CA_2—CB_2 | 1.533 (3) |
C4—C5 | 1.382 (4) | CA_2—C_2 | 1.547 (3) |
C4—H4 | 0.98 (3) | CB_2—HB1_2 | 0.95 (3) |
C5—C6 | 1.384 (3) | CB_2—HB2_2 | 0.92 (3) |
C5—H5 | 1.08 (3) | CB_2—HB3_2 | 0.96 (5) |
C6—H6 | 0.95 (4) | CG_2—HG1_2 | 0.91 (3) |
C7—O1 | 1.451 (3) | CG_2—HG2_2 | 0.89 (3) |
C7—H71 | 1.10 (4) | CG_2—HG3_2 | 0.96 (4) |
C7—H72 | 1.03 (4) | C_2—O2_2 | 1.241 (3) |
O1—C | 1.339 (2) | C_2—O1_2 | 1.252 (2) |
C—O | 1.232 (2) | O2_2—Ca_3 | 2.2343 (16) |
C—N_1 | 1.317 (3) | Ca_3—O2_2i | 2.2342 (16) |
O—Ca_3 | 2.3200 (16) | Ca_3—Oi | 2.3200 (16) |
N_1—CA_1 | 1.441 (2) | Ca_3—O_4i | 2.3702 (18) |
N_1—H_1 | 0.90 (3) | Ca_3—O_4 | 2.3702 (17) |
CA_1—C_1 | 1.522 (3) | O_4—H1_4 | 1.00 (5) |
CA_1—HA1_1 | 0.93 (3) | O_4—H2_4 | 1.07 (6) |
C6—C1—C2 | 119.0 (2) | C_1—N_2—H_2 | 113 (3) |
C6—C1—C7 | 120.2 (2) | CA_2—N_2—H_2 | 123 (3) |
C2—C1—C7 | 120.7 (2) | N_2—CA_2—CG_2 | 110.34 (19) |
C3—C2—C1 | 120.4 (2) | N_2—CA_2—CB_2 | 106.75 (16) |
C3—C2—H2 | 122.9 (19) | CG_2—CA_2—CB_2 | 110.68 (19) |
C1—C2—H2 | 116.7 (19) | N_2—CA_2—C_2 | 110.43 (16) |
C2—C3—C4 | 120.1 (2) | CG_2—CA_2—C_2 | 112.33 (17) |
C2—C3—H3 | 119.1 (19) | CB_2—CA_2—C_2 | 106.08 (19) |
C4—C3—H3 | 121 (2) | CA_2—CB_2—HB1_2 | 103.5 (18) |
C5—C4—C3 | 119.6 (2) | CA_2—CB_2—HB2_2 | 107.3 (18) |
C5—C4—H4 | 122.3 (19) | HB1_2—CB_2—HB2_2 | 112 (3) |
C3—C4—H4 | 118.0 (19) | CA_2—CB_2—HB3_2 | 113 (3) |
C4—C5—C6 | 120.3 (2) | HB1_2—CB_2—HB3_2 | 113 (3) |
C4—C5—H5 | 124.7 (18) | HB2_2—CB_2—HB3_2 | 107 (3) |
C6—C5—H5 | 115.0 (18) | CA_2—CG_2—HG1_2 | 110 (2) |
C1—C6—C5 | 120.5 (2) | CA_2—CG_2—HG2_2 | 113 (2) |
C1—C6—H6 | 117 (2) | HG1_2—CG_2—HG2_2 | 107 (3) |
C5—C6—H6 | 122 (2) | CA_2—CG_2—HG3_2 | 107 (2) |
O1—C7—C1 | 106.06 (19) | HG1_2—CG_2—HG3_2 | 107 (3) |
O1—C7—H71 | 101.6 (18) | HG2_2—CG_2—HG3_2 | 114 (3) |
C1—C7—H71 | 116.7 (18) | O2_2—C_2—O1_2 | 124.2 (2) |
O1—C7—H72 | 102 (2) | O2_2—C_2—CA_2 | 117.83 (18) |
C1—C7—H72 | 115 (2) | O1_2—C_2—CA_2 | 117.76 (18) |
H71—C7—H72 | 113 (3) | C_2—O2_2—Ca_3 | 171.82 (15) |
C—O1—C7 | 115.48 (17) | O2_2i—Ca_3—O2_2 | 180.0 |
O—C—N_1 | 123.95 (19) | O2_2i—Ca_3—Oi | 94.24 (6) |
O—C—O1 | 123.3 (2) | O2_2—Ca_3—Oi | 85.75 (6) |
N_1—C—O1 | 112.70 (17) | Oi—Ca_3—O | 180.0 |
C—O—Ca_3 | 156.34 (15) | O—Ca_3—O2_2 | 94.24 (6) |
C—N_1—CA_1 | 119.38 (17) | Oi—Ca_3—O2_2 | 85.76 (6) |
C—N_1—H_1 | 120 (2) | O—Ca_3—O_4 | 86.79 (6) |
CA_1—N_1—H_1 | 121 (2) | O—Ca_3—O_4i | 93.21 (6) |
N_1—CA_1—C_1 | 111.96 (16) | O2_2—Ca_3—O_4 | 86.27 (7) |
N_1—CA_1—HA1_1 | 108.0 (16) | O2_2—Ca_3—O_4i | 93.73 (7) |
C_1—CA_1—HA1_1 | 113.1 (17) | O2_2i—Ca_3—O_4 | 93.73 (7) |
N_1—CA_1—HA2_1 | 109.4 (18) | O2_2—Ca_3—O_4 | 86.27 (7) |
C_1—CA_1—HA2_1 | 105.6 (19) | Oi—Ca_3—O_4 | 93.21 (6) |
HA1_1—CA_1—HA2_1 | 109 (3) | O—Ca_3—O_4 | 86.79 (6) |
O_1—C_1—N_2 | 123.21 (18) | O_4i—Ca_3—O_4 | 180.0 |
O_1—C_1—CA_1 | 122.38 (17) | Ca_3—O_4—H1_4 | 122 (3) |
N_2—C_1—CA_1 | 114.41 (17) | Ca_3—O_4—H2_4 | 128 (3) |
C_1—N_2—CA_2 | 122.52 (17) | H1_4—O_4—H2_4 | 101 (4) |
Symmetry code: (i) −x, −y, −z+1. |
D—H···A | D—H | H···A | D···A | D—H···A |
N_1—H_1···O_1ii | 0.90 (3) | 1.91 (3) | 2.800 (2) | 169 (3) |
N_2—H_2···O1_2iii | 0.73 (4) | 2.18 (4) | 2.864 (2) | 156 (4) |
O_4—H1_4···O1_2iii | 1.00 (5) | 1.75 (6) | 2.741 (3) | 172 (5) |
O_4—H2_4···Oiv | 1.07 (6) | 1.99 (6) | 3.053 (2) | 176 (6) |
Symmetry codes: (ii) −x, y−1/2, −z+1/2; (iii) x, y−1, z; (iv) −x, −y−1, −z+1. |
C14H18N2O5 | Dx = 1.397 Mg m−3 |
Mr = 294.30 | Cu Kα radiation, λ = 1.54178 Å |
Orthorhombic, Pbca | Cell parameters from 312 reflections |
a = 9.5260 (19) Å | θ = 3.1–44.6° |
b = 28.608 (6) Å | µ = 0.90 mm−1 |
c = 10.270 (2) Å | T = 100 K |
V = 2798.8 (10) Å3 | Plate, colourless |
Z = 8 | 0.2 × 0.1 × 0.05 mm |
F(000) = 1248 |
Bruker Venture D8 diffractometer | 2522 reflections with I > 2σ(I) |
profile data from φ or ω scans | Rint = 0.067 |
Absorption correction: multi-scan (SADABS; Bruker, 2008) | θmax = 77.7°, θmin = 3.1° |
Tmin = 0.90, Tmax = 0.96 | h = −11→12 |
44443 measured reflections | k = −36→36 |
2843 independent reflections | l = −12→13 |
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Hydrogen site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.036 | All H-atom parameters refined |
wR(F2) = 0.090 | w = 1/[σ2(Fo2) + (0.0396P)2 + 1.1904P] where P = (Fo2 + 2Fc2)/3 |
S = 1.09 | (Δ/σ)max = 0.001 |
2843 reflections | Δρmax = 0.27 e Å−3 |
262 parameters | Δρmin = −0.21 e Å−3 |
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes. |
x | y | z | Uiso*/Ueq | ||
C1 | 0.96843 (14) | 0.33651 (5) | 0.17611 (13) | 0.0204 (3) | |
C2 | 0.91669 (14) | 0.31322 (5) | 0.06711 (13) | 0.0220 (3) | |
H2 | 0.8387 (18) | 0.3269 (6) | 0.0193 (16) | 0.027 (4)* | |
C3 | 0.97610 (15) | 0.27138 (5) | 0.02714 (14) | 0.0257 (3) | |
H3 | 0.9404 (18) | 0.2549 (6) | −0.0516 (17) | 0.030 (4)* | |
C4 | 1.08684 (15) | 0.25222 (5) | 0.09657 (16) | 0.0287 (3) | |
H4 | 1.130 (2) | 0.2242 (7) | 0.0670 (18) | 0.042 (5)* | |
C5 | 1.13629 (16) | 0.27456 (5) | 0.20693 (15) | 0.0302 (3) | |
H5 | 1.2082 (19) | 0.2620 (6) | 0.2553 (18) | 0.031 (4)* | |
C6 | 1.07709 (15) | 0.31656 (5) | 0.24705 (14) | 0.0259 (3) | |
H6 | 1.1110 (17) | 0.3317 (6) | 0.3233 (16) | 0.024 (4)* | |
C7 | 0.90948 (16) | 0.38351 (5) | 0.21154 (15) | 0.0262 (3) | |
H71 | 0.810 (2) | 0.3851 (6) | 0.1938 (16) | 0.026 (4)* | |
H72 | 0.9308 (18) | 0.3923 (6) | 0.3014 (18) | 0.030 (4)* | |
O1 | 0.96954 (10) | 0.41880 (3) | 0.12554 (9) | 0.0222 (2) | |
C | 1.06743 (13) | 0.44778 (4) | 0.17393 (12) | 0.0163 (3) | |
O | 1.10316 (10) | 0.45014 (3) | 0.28856 (9) | 0.0215 (2) | |
N_1 | 1.12335 (11) | 0.47415 (4) | 0.07933 (10) | 0.0158 (2) | |
H_1 | 1.0918 (19) | 0.4703 (6) | −0.0046 (19) | 0.033 (5)* | |
CA_1 | 1.20786 (12) | 0.51416 (4) | 0.11432 (12) | 0.0161 (2) | |
H1_1 | 1.2928 (17) | 0.5050 (5) | 0.1588 (15) | 0.017 (4)* | |
H2_1 | 1.2366 (16) | 0.5302 (6) | 0.0336 (15) | 0.020 (4)* | |
C_1 | 1.12366 (12) | 0.54897 (4) | 0.19605 (11) | 0.0138 (2) | |
O_1 | 0.99489 (9) | 0.55194 (3) | 0.18472 (8) | 0.0163 (2) | |
N_2 | 1.19880 (11) | 0.57585 (4) | 0.27582 (10) | 0.0147 (2) | |
H_2 | 1.287 (2) | 0.5720 (6) | 0.2796 (16) | 0.026 (4)* | |
CA_2 | 1.13637 (12) | 0.61511 (4) | 0.34700 (12) | 0.0153 (2) | |
CB_2 | 1.24310 (14) | 0.63395 (5) | 0.44538 (13) | 0.0209 (3) | |
HB1_2 | 1.2728 (17) | 0.6095 (6) | 0.5053 (16) | 0.026 (4)* | |
HB2_2 | 1.200 (2) | 0.6593 (7) | 0.4966 (17) | 0.036 (5)* | |
HB3_2 | 1.3238 (19) | 0.6467 (6) | 0.4009 (16) | 0.028 (4)* | |
CG_2 | 1.09477 (15) | 0.65365 (5) | 0.25267 (14) | 0.0220 (3) | |
HG1_2 | 1.0301 (19) | 0.6422 (6) | 0.1863 (16) | 0.029 (4)* | |
HG2_2 | 1.0499 (19) | 0.6787 (7) | 0.2964 (18) | 0.032 (5)* | |
HG3_2 | 1.1808 (19) | 0.6660 (6) | 0.2125 (16) | 0.028 (4)* | |
C_2 | 1.01118 (13) | 0.59836 (4) | 0.42891 (11) | 0.0161 (3) | |
O_2 | 0.90772 (9) | 0.62163 (3) | 0.44834 (9) | 0.0226 (2) | |
OH_2 | 1.03729 (10) | 0.55748 (3) | 0.48645 (9) | 0.0193 (2) | |
HH_2 | 0.976 (2) | 0.5538 (7) | 0.550 (2) | 0.045 (6)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.0193 (6) | 0.0213 (6) | 0.0207 (6) | −0.0080 (5) | 0.0065 (5) | 0.0012 (5) |
C2 | 0.0197 (6) | 0.0257 (7) | 0.0206 (6) | −0.0036 (5) | 0.0020 (5) | 0.0004 (5) |
C3 | 0.0259 (7) | 0.0256 (7) | 0.0257 (7) | −0.0064 (6) | 0.0056 (6) | −0.0044 (6) |
C4 | 0.0263 (7) | 0.0212 (7) | 0.0385 (8) | −0.0012 (6) | 0.0107 (6) | 0.0023 (6) |
C5 | 0.0215 (7) | 0.0322 (8) | 0.0368 (8) | −0.0019 (6) | −0.0009 (6) | 0.0102 (6) |
C6 | 0.0227 (7) | 0.0310 (7) | 0.0241 (7) | −0.0107 (6) | −0.0011 (5) | 0.0025 (6) |
C7 | 0.0266 (8) | 0.0227 (7) | 0.0294 (7) | −0.0089 (6) | 0.0121 (6) | −0.0028 (6) |
O1 | 0.0218 (5) | 0.0211 (5) | 0.0237 (5) | −0.0070 (4) | 0.0022 (4) | −0.0006 (4) |
C | 0.0127 (6) | 0.0159 (6) | 0.0204 (6) | 0.0032 (4) | 0.0028 (5) | −0.0015 (4) |
O | 0.0193 (5) | 0.0266 (5) | 0.0186 (5) | −0.0008 (4) | 0.0012 (3) | 0.0018 (4) |
N_1 | 0.0144 (5) | 0.0170 (5) | 0.0160 (5) | −0.0009 (4) | 0.0012 (4) | −0.0014 (4) |
CA_1 | 0.0101 (6) | 0.0188 (6) | 0.0193 (6) | −0.0005 (5) | 0.0024 (5) | −0.0010 (5) |
C_1 | 0.0115 (6) | 0.0149 (6) | 0.0150 (5) | −0.0001 (4) | 0.0016 (4) | 0.0024 (4) |
O_1 | 0.0089 (4) | 0.0206 (4) | 0.0194 (4) | 0.0003 (3) | 0.0008 (3) | −0.0027 (3) |
N_2 | 0.0072 (5) | 0.0183 (5) | 0.0186 (5) | 0.0014 (4) | 0.0002 (4) | −0.0017 (4) |
CA_2 | 0.0119 (5) | 0.0164 (6) | 0.0177 (6) | 0.0014 (4) | −0.0006 (4) | −0.0020 (5) |
CB_2 | 0.0150 (6) | 0.0227 (6) | 0.0249 (7) | −0.0031 (5) | −0.0022 (5) | −0.0048 (5) |
CG_2 | 0.0223 (7) | 0.0194 (6) | 0.0242 (6) | 0.0022 (5) | 0.0002 (5) | 0.0025 (5) |
C_2 | 0.0137 (6) | 0.0198 (6) | 0.0148 (6) | −0.0004 (5) | −0.0025 (4) | −0.0031 (4) |
O_2 | 0.0141 (4) | 0.0288 (5) | 0.0250 (5) | 0.0056 (4) | 0.0014 (3) | −0.0031 (4) |
OH_2 | 0.0170 (4) | 0.0220 (5) | 0.0190 (4) | 0.0000 (3) | 0.0025 (4) | 0.0025 (4) |
C1—C6 | 1.388 (2) | CA_1—C_1 | 1.5296 (16) |
C1—C2 | 1.3929 (19) | CA_1—H1_1 | 0.966 (16) |
C1—C7 | 1.502 (2) | CA_1—H2_1 | 0.987 (16) |
C2—C3 | 1.386 (2) | C_1—O_1 | 1.2351 (15) |
C2—H2 | 0.972 (18) | C_1—N_2 | 1.3322 (16) |
C3—C4 | 1.386 (2) | N_2—CA_2 | 1.4662 (15) |
C3—H3 | 0.996 (18) | N_2—H_2 | 0.85 (2) |
C4—C5 | 1.384 (2) | CA_2—CG_2 | 1.5203 (17) |
C4—H4 | 0.95 (2) | CA_2—CB_2 | 1.5314 (17) |
C5—C6 | 1.390 (2) | CA_2—C_2 | 1.5360 (17) |
C5—H5 | 0.919 (18) | CB_2—HB1_2 | 0.973 (17) |
C6—H6 | 0.951 (17) | CB_2—HB2_2 | 0.987 (19) |
C7—O1 | 1.4583 (16) | CB_2—HB3_2 | 0.966 (18) |
C7—H71 | 0.963 (18) | CG_2—HG1_2 | 0.975 (18) |
C7—H72 | 0.978 (18) | CG_2—HG2_2 | 0.948 (19) |
O1—C | 1.3431 (16) | CG_2—HG3_2 | 0.984 (18) |
C—O | 1.2274 (16) | C_2—O_2 | 1.2061 (15) |
C—N_1 | 1.3403 (16) | C_2—OH_2 | 1.3336 (16) |
N_1—CA_1 | 1.4449 (16) | OH_2—HH_2 | 0.89 (2) |
N_1—H_1 | 0.92 (2) | ||
C6—C1—C2 | 119.27 (13) | C_1—CA_1—H1_1 | 110.9 (9) |
C6—C1—C7 | 121.31 (13) | N_1—CA_1—H2_1 | 108.3 (9) |
C2—C1—C7 | 119.38 (13) | C_1—CA_1—H2_1 | 107.7 (9) |
C3—C2—C1 | 120.44 (13) | H1_1—CA_1—H2_1 | 106.9 (13) |
C3—C2—H2 | 120.6 (10) | O_1—C_1—N_2 | 123.49 (11) |
C1—C2—H2 | 118.9 (10) | O_1—C_1—CA_1 | 120.93 (11) |
C2—C3—C4 | 119.99 (14) | N_2—C_1—CA_1 | 115.56 (10) |
C2—C3—H3 | 120.7 (10) | C_1—N_2—CA_2 | 122.06 (10) |
C4—C3—H3 | 119.3 (10) | C_1—N_2—H_2 | 119.0 (11) |
C5—C4—C3 | 119.85 (14) | CA_2—N_2—H_2 | 118.6 (11) |
C5—C4—H4 | 120.3 (12) | N_2—CA_2—CG_2 | 110.09 (10) |
C3—C4—H4 | 119.8 (12) | N_2—CA_2—CB_2 | 109.22 (10) |
C4—C5—C6 | 120.26 (14) | CG_2—CA_2—CB_2 | 109.77 (11) |
C4—C5—H5 | 121.0 (11) | N_2—CA_2—C_2 | 110.42 (10) |
C6—C5—H5 | 118.7 (11) | CG_2—CA_2—C_2 | 111.90 (10) |
C1—C6—C5 | 120.16 (14) | CB_2—CA_2—C_2 | 105.30 (10) |
C1—C6—H6 | 119.9 (10) | CA_2—CB_2—HB1_2 | 111.0 (10) |
C5—C6—H6 | 119.9 (10) | CA_2—CB_2—HB2_2 | 109.4 (11) |
O1—C7—C1 | 109.05 (11) | HB1_2—CB_2—HB2_2 | 108.2 (14) |
O1—C7—H71 | 103.7 (10) | CA_2—CB_2—HB3_2 | 110.5 (10) |
C1—C7—H71 | 111.4 (10) | HB1_2—CB_2—HB3_2 | 109.8 (14) |
O1—C7—H72 | 108.1 (10) | HB2_2—CB_2—HB3_2 | 108.0 (15) |
C1—C7—H72 | 112.4 (11) | CA_2—CG_2—HG1_2 | 111.5 (10) |
H71—C7—H72 | 111.7 (14) | CA_2—CG_2—HG2_2 | 111.3 (11) |
C—O1—C7 | 118.40 (11) | HG1_2—CG_2—HG2_2 | 107.5 (15) |
O—C—N_1 | 123.65 (12) | CA_2—CG_2—HG3_2 | 108.1 (10) |
O—C—O1 | 125.54 (12) | HG1_2—CG_2—HG3_2 | 110.8 (14) |
N_1—C—O1 | 110.80 (11) | HG2_2—CG_2—HG3_2 | 107.6 (15) |
C—N_1—CA_1 | 119.15 (10) | O_2—C_2—OH_2 | 124.28 (12) |
C—N_1—H_1 | 118.8 (11) | O_2—C_2—CA_2 | 123.55 (11) |
CA_1—N_1—H_1 | 120.7 (11) | OH_2—C_2—CA_2 | 111.81 (10) |
N_1—CA_1—C_1 | 111.11 (10) | C_2—OH_2—HH_2 | 107.8 (13) |
N_1—CA_1—H1_1 | 111.7 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N_1—H_1···O_1i | 0.92 (2) | 2.12 (2) | 3.0298 (14) | 168.7 (16) |
N_2—H_2···O_1ii | 0.85 (2) | 2.09 (2) | 2.9304 (15) | 167.3 (18) |
OH_2—HH_2···Oiii | 0.88 (2) | 1.82 (2) | 2.6789 (14) | 162 (2) |
Symmetry codes: (i) −x+2, −y+1, −z; (ii) x+1/2, y, −z+1/2; (iii) −x+2, −y+1, −z+1. |
Acknowledgements
We are grateful to Dr Danny Axford for assistance at Diamond beamline I24 during the data collection and to Aleka Manousaki for measurements using the EDS facility of IESL–FORTH, Heraklion.
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