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![[Figure 7]](qe5003fig7mag.jpg)
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Figure 7
High-energy ring conformations may cause glycosidic link anomalies. The MAN(F7)–BMA(F3) linkage (red asterisk in the bottom panel) of PDB entry 5gsq (Chen et al., 2017  ; gold), which was not part of the curated torsion-angle data set because the MAN residue has a poor RSCC, is identified as an outlier (φ = −3.0°, ψ = 122.6°). BMA (chain ID and sequence number F3) and MAN (chain ID and sequence number F7) are represented by a ball-and-stick model (C, green; O, red), whilst the rest of the attached glycan is shown in a faded grey ball-and-stick representation. Residues identified as interacting with the linkage are represented in stick form (C, gold; O, red; N, blue). Hydrogen bonds (black dashed lines) are shown with the distance between atoms in Å. 2Fo − Fc electron density (grey) is displayed for the linkage contoured to 1σ. Possible CH–π interactions were identified and can be seen between Phe243 and NAG(F5) and between Phe241 and BMA(F3). This linkage has a Z-score of −1.32, and presumably became distorted because the terminal mannose, MAN(F7), is in a 1S3 skew-boat ring conformation (high energy; for further reading on conformational anomalies, please refer to Agirre, Davies et al., 2015), as also highlighted in orange in the figure, due to the absence of well defined electron density. Both the linkage and ring conformations are unsupported by the electron density and should be either removed or corrected before deposition to reflect the most probable, low-energy conformations. The top image was produced using CCP4mg. Bottom: SNFG notation output from Privateer. |
![[Figure 7]](qe5003fig7.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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