engleski

Divalent metal cations in proteins: abundance, coordination, function

For the purpose of gaining beter insight into possible enviroment of the divalent metal ions that are frequently present in poteins we performed an exhaustive serach of the PDB. Since Protein data base contains number of structures of the same protein (free or complexed or it mutants, or the same protein from different organisms) we have not performed the serach on the whole data set, but on the smaller set of non-redundant set of proteins. Proteins from PDB were clustered according to their similarity, i.e. all proteins with sequence identity of 70% or higher were grouped in clusters, From each cluster we chose the best ranking chain (and the corresponding PDB file) and checked if any of the following metal cations: Cu+2, Zn+2, Mg+2, Mn+2, Fe+2, Co+2, Cd+2 and Ca+2 is bound. This resulted with a set of the 9400 proteins. In this way we obtained a representative set of proteins which 3D structure is solved.

metal; proteins

nije evidentirano