MeRNA: a Database of Metal Ion Binding Sites in RNAStructures

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Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using ... continued below

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Stefan, Liliana R.; Zhang, Rui; Levitan, Aaron G.; Hendrix, DonnaF.; Brenner, Steven E. & Holbrook, Stephen R. October 5, 2005.

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Metal ions are essential for the folding of RNA into stable tertiary structures and for the catalytic activity of some RNA enzymes. To aid in the study of the roles of metal ions in RNA structural biology, we have created MeRNA (Metals in RNA), a comprehensive compilation of all metal binding sites identified in RNA three-dimensional structures available from the Protein Data Bank (PDB) and Nucleic Acid Database (NDB). Currently, our database contains information relating to binding of 9764 metal ions corresponding to 23 distinct elements; in 256 RNA structures. The metal ion locations were confirmed and ligands characterized using original literature references. MeRNA includes eight manually identified metal-ion binding motifs, which are described in the literature. MeRNA is searchable by PDB identifier, metal ion, method of structure determination, resolution and R-values for X-ray structure, and distance from metal to any RNA atom or to water. New structures with their respective binding motifs will be added to the database as they become available. The MeRNA database will further our understanding of the roles of metal ions in RNA folding and catalysis and have applications in structural and functional analysis, RNA design and engineering.

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  • Journal Name: Nucleic Acids Research; Journal Volume: 34; Related Information: Journal Publication Date: 2006

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  • Report No.: LBNL--58971
  • Grant Number: DE-AC02-05CH11231
  • Grant Number: NIH:1R01GM66199,1R01HG002665,K22HG00056
  • Office of Scientific & Technical Information Report Number: 901029
  • Archival Resource Key: ark:/67531/metadc890573

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  • October 5, 2005

Added to The UNT Digital Library

  • Sept. 22, 2016, 2:13 a.m.

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  • Dec. 15, 2016, 1:26 p.m.

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Stefan, Liliana R.; Zhang, Rui; Levitan, Aaron G.; Hendrix, DonnaF.; Brenner, Steven E. & Holbrook, Stephen R. MeRNA: a Database of Metal Ion Binding Sites in RNAStructures, article, October 5, 2005; Berkeley, California. (digital.library.unt.edu/ark:/67531/metadc890573/: accessed September 21, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.