Validation and correction of Zn–Cys _x His _y complexes

Abstract

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

ISOLDE: a physically realistic environment for model building into low-resolution electron-density maps

“…In future versions of ISOLDE I plan to add metal-coordination bond/angle restraints to improve the handling of such situations. The need for improved handling of metal interactions is not unique to MD, as has been recently discussed in the context of crystallographic refinement of zinccoordination sites (Touw et al, 2016).…”

CheckMyMetal: a macromolecular metal-binding validation tool

“…Zn-S distances increase from 2.30 to 2.33 Å as the number of cysteines increases from one to four, and Zn-N distances also increase from 2.00 to 2.07 Å as the number of cysteines that coordinate the zinc increases from one to three. As the number of cysteines in the first coordination sphere increases from two to four, the S-Zn-S angles decrease from 116 to 109 (Touw et al, 2016).…”

“…In zinc-binding sites coordinated by only cysteine and histidine, the Zn-ligand distances and S-Zn-S angles are correlated with the number of cysteines and histidines (Touw et al, 2016). Zn-S distances increase from 2.30 to 2.33 Å as the number of cysteines increases from one to four, and Zn-N distances also increase from 2.00 to 2.07 Å as the number of cysteines that coordinate the zinc increases from one to three.…”

“…From the default values in the CCP4 library (ener_lib.cif) used by most popular macromoleculerefinement programs (Table 2), the Zn-N distance restraint (2.15 Å ) would only be correct for six-coordinated zinc. Fourcoordinated zinc should show a Zn-N distance between 2.00 and 2.07 Å (Touw et al, 2016). Therefore, one should pay extra attention to the possible presence of incorrectly restrained Zn-N distances when examining zinc-binding sites in the PDB.…”

AceDRG: a stereochemical description generator for ligands

“…Therefore, metal-containing compounds may require another level of abstraction, where the surrounding atoms can be exchanged with other atoms without affecting local geometry. Some work towards contextdependent metal-coordination behaviour has been discussed by Touw et al (2016).…”