title: MINAS--a database of Metal Ions in Nucleic AcidS.
abstract: Correctly folded into the respective native 3D structure, RNA and DNA are responsible for uncountable key functions in any viable organism. In order to exert their function, metal ion cofactors are closely involved in folding, structure formation and, e.g. in ribozymes, also the catalytic mechanism. The database MINAS, Metal Ions in Nucleic AcidS (http://www.minas.uzh.ch), compiles the detailed information on innersphere, outersphere and larger coordination environment of >70,000 metal ions of 36 elements found in >2000 structures of nucleic acids contained today in the PDB and NDB. MINAS is updated monthly with new structures and offers a multitude of search functions, e.g. the kind of metal ion, metal-ligand distance, innersphere and outersphere ligands defined by element or functional group, residue, experimental method, as well as PDB entry-related information. The results of each search can be saved individually for later use with so-called miniPDB files containing the respective metal ion together with the coordination environment within a 15 Å radius. MINAS thus offers a unique way to explore the coordination geometries and ligands of metal ions together with the respective binding pockets in nucleic acids.
authors.affiliation: Institute of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.
authors.forename: Joachim
authors.initials: J
authors.lastname: Schnabl
authors.forename: Pascal
authors.initials: P
authors.lastname: Suter
authors.forename: Roland K O
authors.initials: RK
authors.lastname: Sigel
mesh_terms: D001665:Binding Sites; D004247:DNA / Q000737:chemistry*; D030561:Databases, Nucleic Acid; D007477:Ions / Q000737:chemistry; D008274:Magnesium / Q000737:chemistry; D008670:Metals / Q000737:chemistry*; D020135:Peptide Nucleic Acids / Q000737:chemistry; D012313:RNA / Q000737:chemistry*
chemical_list: D007477:Ions; D008670:Metals; D020135:Peptide Nucleic Acids; D012313:RNA; D004247:DNA; D008274:Magnesium
references.citation: Nucleic Acids Res. 2004 Jan 1;32(Database issue):D182-4
references.pmid: 14681389
references.citation: Cell. 1983 Dec;35(3 Pt 2):849-57
references.pmid: 6197186
references.citation: Chem Rev. 2007 Jan;107(1):97-113
references.pmid: 17212472
references.citation: Mol Cell. 2006 Nov 17;24(4):611-7
references.pmid: 17188036
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D392-401
references.pmid: 21036868
references.citation: Nucleic Acids Res. 2006 Jan 1;34(Database issue):D131-4
references.pmid: 16381830
references.citation: Annu Rev Biochem. 2009;78:305-34
references.pmid: 19298181
references.citation: Cell. 1982 Nov;31(1):147-57
references.pmid: 6297745
references.citation: Bioinformatics. 2007 Apr 15;23(8):1035-7
references.pmid: 17324939
references.citation: J Mol Biol. 2007 Sep 28;372(4):942-957
references.pmid: 17707400
references.citation: Curr Opin Chem Biol. 2010 Apr;14(2):269-75
references.pmid: 20047851
references.citation: Met Ions Life Sci. 2012;10:1-42
references.pmid: 22210334
references.citation: Nucleic Acids Res. 2000 Jan 1;28(1):235-42
references.pmid: 10592235
references.citation: Biochem Mol Biol Educ. 2006 Jul;34(4):255-61
references.pmid: 21638687