Metals in protein structures: a review of their principal features
Metals are present in more than one-third of all proteins as they occur in nature, and are usually important in biological function or maintenance of the structure. Some are present as cations, directly associated with amino acid functional groups of the protein, others within small molecule cofactors associated with the protein. For the 10 metals commonly found as cations, Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu and Zn, a survey is given of occurrence, relative frequencies of both metal and donor atom or group type, and geometry of coordination. The survey is based on crystal structure information deposited in the Protein Data Bank (PDB) [Berman, H.; Henrick, K.; Nakamura, H.; Markley, J.L. The Worldwide Protein Data Bank (wwPDB): Ensuring a Single, Uniform Archive of PDB Data. Nucleic Acids Res. 2007, 35, D301–D303]. The precision and reliability of this information is assessed in detail. Illustrative examples are given for each metal, including, usually, details of the structure of the metal site in relation to the whole protein and to its function; there are comparisons between metals and descriptions of features such as binding to carboxylate and multiple metal sites close to each other. Metals found within cofactors which associate with the protein, most notably Mo, are included within these examples. Also included briefly are the prediction of metal sites in proteins resulting from genomic synthesis, information which can be derived from methods other than X-ray diffraction of crystals, and metal–protein systems which do not occur naturally.