 | Acta Crystallographica Section D Acta Crystallographica Section D BIOLOGICAL CRYSTALLOGRAPHY |
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![[Figure 3]](rr5017fig3mag.jpg)
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Figure 3
The region near ADP A811 in PDB entry 3pdt is shown in (a) as originally refined in REFMAC. All H atoms were added to this model and their positions were minimized while holding non-H atoms fixed, but only some of these H atoms are shown for clarity. Multiple clashes between the misplaced residue GlnA758 and PheA720 were apparently tolerated in the REFMAC refinement. The close contacts (orange dashed lines) were so severe that the energy minimization distorted the planarity of the aromatic system rather than allowing the higher energy interpenetration of atoms. The position of these two residues after refinement with PrimeX is shown in (b). In order to relieve the strain of the clash, the LysA722 side chain moved toward the ligand with a coordinated motion of the glutamine side chain into its correct position in strong electron density below the Lys residue. Hydrogen bonds are shown as purple dashed lines. The electron-density grid for this region is contoured at 1.0σ from a 2Fo − Fc composite OMIT map. |
![[Figure 3]](rr5017fig3.jpg)
| BIOLOGICAL CRYSTALLOGRAPHY |
ISSN: 1399-0047
