title: Validation and correction of Zn-CysxHisycomplexes.
abstract: Many crystal structures in the Protein Data Bank contain zinc ions in a geometrically distorted tetrahedral complex with four Cys and/or His ligands. A method is presented to automatically validate and correct these zinc complexes. Analysis of the corrected zinc complexes shows that the average Zn-Cys distances and Cys-Zn-Cys angles are a function of the number of cysteines and histidines involved. The observed trends can be used to develop more context-sensitive targets for model validation and refinement.
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Wouter G
authors.initials: WG
authors.lastname: Touw
authors.affiliation: Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Bart
authors.initials: B
authors.lastname: van Beusekom
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Jochem M G
authors.initials: JM
authors.lastname: Evers
authors.affiliation: Centre for Molecular and Biomolecular Informatics, Radboud University Medical Center, Geert Grooteplein-Zuid 26-28, 6525 GA Nijmegen, The Netherlands.
authors.forename: Gert
authors.initials: G
authors.lastname: Vriend
authors.affiliation: Department of Biochemistry, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX Amsterdam, The Netherlands.
authors.forename: Robbie P
authors.initials: RP
authors.lastname: Joosten
mesh_terms: D001665:Binding Sites; D056831:Coordination Complexes / Q000737:chemistry; D018360:Crystallography, X-Ray; D003545:Cysteine / Q000737:chemistry*; D030562:Databases, Protein; D006639:Histidine / Q000737:chemistry*; D008024:Ligands; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry*; D015032:Zinc / Q000737:chemistry*
chemical_list: D056831:Coordination Complexes; D008024:Ligands; D011506:Proteins; D006639:Histidine; D015032:Zinc; D003545:Cysteine
keywords: geometric restraints; protein zinc-binding site; refinement; validation; zinc metal-site geometry