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![[Figure 4]](ir5021fig4mag.jpg)
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Figure 4
Description of the covalent linkage of N-acetylglucosamine (NAG) and asparagine (ASN) using AceDRG. (a) Chemical diagrams of the individual NAG and ASN components (from the CCP4-ML) and (b) the linked composite compound, in which the covalent linkage is depicted as a dotted line (created using ChemDraw Professional 17.1). (c) Comparison of a deposited 2.4 Å resolution model (PDB entry 3kwf; Mattei et al., 2010  ; purple) and the model re-refined with REFMAC5 using an AceDRG link dictionary (green), focusing on NAG-A796 and ASN-A229, displayed using Coot. Interatomic distances and dotted lines corresponding to the linkage are shown for both models (note that the deposited model did not contain a corresponding link record). The 2mFo − DFc map corresponding to the re-refined model is shown as a grey mesh. Transparent surfaces surrounding atoms in the linked complex highlight the atoms involved in link-dictionary restraints, corresponding to (d) changes in bond/angle/chirality restraints (red surface), (e) torsion-angle restraints (green), (f) planar restraints that are removed (blue) and (g) planar restraints that are added (gold) due to the covalent linkage. H atoms were modelled in riding positions using REFMAC5. |
![[Figure 4]](ir5021fig4.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
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