Journal of Molecular Modeling

, Volume 17, Issue 3, pp 429–442

Metals in proteins: cluster analysis studies

Original Paper

DOI: 10.1007/s00894-010-0733-5

Cite this article as:
Tamames, J.A.C. & Ramos, M.J. J Mol Model (2011) 17: 429. doi:10.1007/s00894-010-0733-5

Abstract

We have conducted a prospective analysis of the Protein Data Bank in order to study certain constituents of proteins: elements that are neither halogens nor phosphorus nor part of the biological amino acid set. A sample of 5749 structures was analyzed and classified according to the 56 elements encountered. Fifteen metals (Na, Mg, K, Ca, Mn, Fe, Co, Ni, Cu, Zn, As, Mo, Cd, W, Hg) are involved in almost half of the structures, with each metal figuring in more than 100 structures. We analyzed this subsample in more detail by computing the amino acid residues occurring within a coordination sphere of 5 Å centered on the element, and using methods of cluster analysis to group the elements. The analyses undertaken here are able to distinguish between real components of proteins and elements inserted by artefacts of the crystallization process or experimental techniques.

Keywords

PDBProteinStatistical analysisCluster analysis

Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  1. 1.Requimente, Departamento de Química, Faculdade de CiênciasUniversidade do PortoPortoPortugal