Validation and correction of Zn–CysxHisy complexes

A method is presented to automatically validate and correct Zn–CysxHisy complexes that have a distorted tetrahedral geometry.


S1. Zn-S and Zn-N distances
Supplementary Table S1. Distances between Zn and S or N are listed as mean ± standard deviation.

Study Zn-S (Å) Zn-N (Å) Databank Resolution (Å) and other criteria
Site type (Alberts et al., 1998)  From left to right are listed the source reference, any Zn-S and Zn-N distances listed, the data source, resolution cut offs when the source was PDB and R-factor cut-offs when the source was CSD, and the type of cluster studied (with all indicating lack of discrimination, SSSS indicates the general case of Zn coordination by four sulphur atoms, and T4 indicating that the coordination number had to be 4). Numbers in brackets indicate the number of observations. *: suggested targets by Harding (2006).

S2. Geometry of ZnCysxHisy sites
Supplementary Figure S1. r.m.s.Z for the five possible ZnCys x His y site types after PDB_REDO rerefinement with and without Zen remediation. PDB and Zen-remediated sites are compared in Fig. 1 in the main text.
Supplementary Figure S2. (next page). Box-and-whisker plots of the Z scores characterizing ZnCys x His y complexes in original PDB (red), PDB_REDO without Zen remediation (green) and PDB_REDO with Zen remediation (blue) structure models. The whiskers extend to the nearest value that is within 1.5 times the inter-quartile range; outliers are marked as dots. The Z score for 'Zn position' indicates the deviation from the expected Zn position in the tetrahedron. 4256 outliers with a Z score smaller than -15 or larger than 15 are not shown for clarity. 2735 of these outliers are from PDB structure models, 1440 are from PDB_REDO without Zen, and 81 are from PDB_REDO with Zen remediation, respectively.   (Ma et al., 2015)]. LINK records between Zn ligands prevent correct refinement. Zen has been adapted to deal with this, fortunately rare, type of problem. (c) Undetected side-chain flips of the Histidines that coordinate Zn504, chain A, of the SAGA Deubiquinating Module [PDB 4fip; 2.69 Å (Samara et al., 2012)].
Supplementary Figure S4. Zn147 in the active site of cytidine deaminase [PDB 1mq0; 2.4 Å (Chung et al., 2005)]. (a) In chain A the mF o -DF c difference density map from PDB_REDO (contoured at +3σ, green, and -3σ, red) within 3 Å of Zn147 indicates that the Zn-coordinating water molecule is missing. (b) The water molecule (O151) has been modelled in chain B. PDB_REDO is correct in not generating restraints between Cys59 and Zn147, but is not yet capable of adding the water in chain A.