Flexibility of metal binding sites in proteins on a database scale.
Protein metal binding sites in the pre-bound (apo) state, and their rearrangements upon metal binding were not analyzed previously at a database scale. Such a study may provide valuable information for metal binding site prediction and design. A high resolution, nonredundant dataset of 210 metal binding sites was created, containing all available representatives of apo-holo pairs for the most populated metals in the PDB. More than 40% of the sites underwent rearrangements upon metal binding. In 30 cases rearrangements involved the backbone. The tendency for side-chain rearrangement inversely correlates with the number of first-shell residues. Analysis of side-chain reorientations as a result of metal binding showed that in 95% of the rigid-backbone binding sites at most one side chain moved. Thus, in general, part of the first coordination shell is already in place in the pre-bound form. The frequencies of side-chain reorientation directly correlated with metal ligand flexibility and solvent accessibility in the apo state.
Babor
Mariana
M
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel.
Greenblatt
Harry M
HM
Edelman
Marvin
M
Sobolev
Vladimir
V
D001059:Apoproteins / Q000737:chemistry / Q000378:metabolism; D001665:Binding Sites; D002118:Calcium / Q000378:metabolism; D030562:Databases, Protein; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D008667:Metalloproteins / Q000737:chemistry* / Q000378:metabolism*; D008670:Metals / Q000737:chemistry / Q000378:metabolism*; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D012997:Solvents; D015032:Zinc / Q000378:metabolism
D001059:Apoproteins; D004798:Enzymes; D008667:Metalloproteins; D008670:Metals; D011506:Proteins; D012997:Solvents; D015032:Zinc; D002118:Calcium