Small revisions to predicted distances around metal sites in proteins.
A new analysis has been made of distances around metal sites in protein structures in the Protein Data Bank determined with resolution < or =1.25 A and equivalent distances have been extracted from the Cambridge Structural Database. They are for the metals Na, Mg, K, Ca, Mn, Fe, Co, Cu, Zn and the donor atoms O of water, O of Asp and Glu, O of the main-chain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of 'target distances' previously given. As well as small changes in many distances and a large improvement for Mg-O(carboxylate), the table includes an indication of how reliable each prediction may be. Special attention was given to carboxylate interactions. When the carboxylate group is monodentate, the M-O(carboxylate) distance is well defined, but for bidentate carboxylate groups a wide range of distances is allowable; when the metal is Co, Cu or Zn the M-O(1) and M-O(2) distances are clearly inversely correlated; for the more purely electrostatic interactions involving Na, K and Ca there is a wider scatter of distances and little correlation.
Harding
Marjorie M
MM
Institute of Structural and Molecular Biology, Michael Swann Building, University of Edinburgh, Edinburgh EH9 3JR, Scotland. marjorie.harding@ed.ac.uk
D001665:Binding Sites; D018360:Crystallography, X-Ray; D030562:Databases, Protein; D008667:Metalloproteins / Q000737:chemistry*; D008670:Metals / Q000737:chemistry*; D015394:Molecular Structure
D008667:Metalloproteins; D008670:Metals