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 <= 1.25 (A) over circle 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 mainchain carbonyl group, N of His and S of Cys. Some revisions are recommended to the tables of 'target distances' previously given [ Harding ( 2001), Acta Cryst. D57, 401-411; Harding ( 2002), Acta Cryst. D58, 872-874]. 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.