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Figure 3
ZnCysxHisy complexes before (left) and after PDB_REDO without (middle) and with (right) Zen remediation. Side chains are coloured by atom type; grey spheres are Zn ions. Figures were prepared with CCP4mg (McNicholas et al., 2011BB46). Electron-density maps were omitted for clarity and are available from the PDB_REDO databank. (a) Zn300, chain A, from the 8-oxoguanine DNA glycosylase MutM (PDB entry 1l1z; 1.7 Å; Fromme & Verdine, 2002BB22). Cys252 points away from the Zn ion. The LINK between Cys252 and Zn was not annotated in the PDB model. In the PDB_REDO models Cys252 Sγ has moved 2.7 Å. Arg251 was refitted to a more plausible conformation only after Zen detected the ZnCys4 site. (b) Zn203, chain I, from the RNA polymerase II–transcription factor IIB complex (PDB entry 1r5u; 4.5 Å; Bushnell et al., 2004BB11). Zn203 is modelled far away from the centre of the four Sγ ligands. The presence of a LINK record between Zn and Cδ2 of Tyr34 and the absence of three Sγ—Zn LINK records in the PDB file precludes complex formation in a standard (re-)refinement. Correction of the Zn site required the Zn to move more than 5 Å. (c) Zn313, chain B, from aspartate transcarbamoylase (PDB entry 3d7s; 2.8 Å; Stieglitz et al., 2009BB60). Several types of cysteine-bridge problems exist in the PDB (Evers et al., 2015BB21), and the four cysteines next to Zn313 form an extreme example. Only three of the four necessary LINK records are specified in the original PDB file and at the same time superfluous SSBOND records are present for three of the six bridges shown. The cysteine clashes are almost resolved even without Zen processing thanks to the adaptations that were made to REFMAC as a result of our work. The additional restraints generated by Zen were necessary to refine the Zn position correctly. (d) Zn4001, chain D, from the DDB1–Cul4A–Rbx1–SV5V complex (PDB entry 2hye; 3.1 Å; Angers et al., 2006BB4). The three cysteines and the histidine are not arranged tetrahedrally around Zn4001 and the three cysteines appear to form one big cysteine bridge. Without Zen remediation the r.m.s.Z is 9.69. The correct Cys42 rotamer was found during re-refinement after processing with Zen, allowing better refinement of the Zn and ligand positions (final r.m.s.Z of 1.09). The Zn4003 site is located close to the Zn4001 site and has a tetrahedral conformation. In the PDB entry the distance from the Cβ atom of Cys53 to Zn4001 is 4.38 Å, whereas the distance to Zn4003 is 4.20 Å. Zen detected correctly that Cys53 only coordinates Zn4003. (e) Zn61, chain B, from the box H/ACA ribonucleoprotein protein particle–RNA complex (PDB entry 3lwq; 2.7 Å; Zhou et al., 2010BB71). Four cysteines are tightly connected near the Zn. In the PDB entry SSBOND records are present for these cysteines, while LINK records for the Zn are found to the backbone N atoms of Gly12 and Lys10. Normal ZnCys4 geometry is obtained in the Zen-processed PDB_REDO model. The ion has moved 3.5 Å. (f) Zn6, chain C, of the Simian virus 40 large T-antigen–human p53 complex (PDB entry 2h1l; 3.2 Å; Lilyestrom et al., 2006BB44). For 12 of the 24 chains in the PDB model SSBOND records are specified between Cys302 and Cys305, while these two residues actually coordinate the Zn together with two histidines. The complex was refined correctly with and without processing by Zen. (g) Zn4, chain B, from the catalytic domain of human AMSH (PDB entry 3rzu; 2.5 Å; Davies et al., 2011BB14). The coordination distances are too large. The distances in the PDB_REDO models were closer to the expected values.

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