Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns.
Zinc is one of the biologically most abundant and important metal elements, present in a plethora of enzymes from a broad array of species of all phyla. In this study we report a thorough analysis of the geometrical properties of Zinc coordination spheres performed on a dataset of 994 high quality protein crystal structures from the Protein Data Bank, and complemented with Quantum mechanical calculations at the DFT level of theory (B3LYP/SDD) on mononuclear model systems. The results allowed us to draw interesting conclusions on the structural characteristics of Zn centres and to evaluate the importance of such effects as the resolution of X-ray crystallographic structures, the enzyme class in which the Zn centre is included, and the identity of the ligands at the Zn coordination sphere. Altogether, the set of results obtained provides useful data for the enhancement of the atomic models normally applied to the theoretical and computational study of zinc enzymes at the quantum mechanical level (in particular enzymatic mechanisms), and for the development of molecular mechanical parameters for the treatment of zinc coordination spheres with molecular mechanics or molecular dynamics in studies with the full enzyme.
Tamames
Bruno
B
REQUIMTE, Departamento de Química, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre 687, 4169-007 Porto, Portugal.
Sousa
Sérgio Filipe
SF
Tamames
Juan
J
Fernandes
Pedro Alexandrino
PA
Ramos
Maria João
MJ
D030562:Databases, Protein; D004798:Enzymes / Q000145:classification; D006801:Humans; D008024:Ligands; D008667:Metalloproteins / Q000737:chemistry*; D011487:Protein Conformation; D015032:Zinc / Q000737:chemistry*
D004798:Enzymes; D008024:Ligands; D008667:Metalloproteins; D015032:Zinc