Metals in proteins: cluster analysis studies

• Type: Article in International Scientific Journal
• Date: 2011

Authors

Juan A C Tamames (Author) Other; Maria Joao Ramos (Author) FCUP

Journal

Title: Journal Of Molecular Modeling

Vol. 17

Pages: 429-442

ISSN: 1610-2940

Publisher: Springer Nature

Indexing

ISI Web of Knowledge - 7 Citations

Scopus - 7 Citations

Scientific classification

FOS: Natural sciences > Chemical sciences

Other information

Authenticus ID: P-002-TED

DOI: 10.1007/s00894-010-0733-5

Abstract (EN): 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 angstrom 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.

Language: English

Type (Professor's evaluation): Scientific

No. of pages: 14