FindGeo: a tool for determining metal coordination geometry

UNLABELLED Metals are essential for the structure and function of many proteins and nucleic acids. The geometrical arrangement of the atoms that coordinate a metal in a biological macromolecule is an important determinant of the specificity and role of that metal. At present, however, this information can be retrieved only from the literature, which sometimes contains an improper or incorrect description of the geometry, and often lacks it altogether. Thus, we developed FindGeo to quickly and easily determine the coordination geometry of selected, or all, metals in a given structure. FindGeo works by superimposing the metal-coordinating atoms in the input structure to a library of templates with alternative ideal geometries, which are ranked by RMSD to identify the best geometry assignment. AVAILABILITY FindGeo is freely available as a web service and as a stand-alone program at http://metalweb.cerm.unifi.it/tools/findgeo/.

[1]  F. Allen.  The Cambridge Structural Database: a quarter of a million crystal structures and rising. , 2002, Acta crystallographica. Section B, Structural science.

[2]  Janet M Thornton,et al.  Structural analysis of metal sites in proteins: non-heme iron sites as a case study. , 2009, Journal of molecular biology.

[3]  Ivano Bertini,et al.  Minimal Functional Sites Allow a Classification of Zinc Sites in Proteins , 2011, PloS one.

[4]  L. Rulíšek,et al.  Coordination geometries of selected transition metal ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in metalloproteins. , 1998, Journal of inorganic biochemistry.

[5]  H. Sigel,et al.  Handbook on Metalloproteins , 2001 .

[6]  S. Kearsley.  On the orthogonal transformation used for structural comparisons , 1989 .

[7]  Jens Müller,et al.  Functional metal ions in nucleic acids. , 2010, Metallomics : integrated biometal science.

[8]  Edward I. Solomon,et al.  Structural and Functional Aspects of Metal Sites in Biology. , 1996, Chemical reviews.

[9]  Roland K. O. Sigel,et al.  From nucleotides to ribozymes—A comparison of their metal ion binding properties , 2007 .

[10]  Dianne Ford,et al.  Metalloproteins and metal sensing , 2009, Nature.

[11]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[12]  Joachim Schnabl,et al.  MINAS—a database of Metal Ions in Nucleic AcidS , 2011, Nucleic Acids Res..

[13]  V. Sobolev,et al.  Prediction of transition metal‐binding sites from apo protein structures , 2007, Proteins.

[14]  Yi Lu,et al.  Design of functional metalloproteins , 2009, Nature.