ArticleJournal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry2004
Structure and binding of Mg(II) ions and di-metal bridge complexes with biological phosphates and phosphoranes.
Article in Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 10 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
10 citing papers in PubMed, 35 citations in OpenAlex.
- Force Field for Mg(2+), Mn(2+), Zn(2+), and Cd(2+) Ions That Have Balanced Interactions with Nucleic Acids.The journal of physical chemistry. B · 2015Article
- Assessment of metal-assisted nucleophile activation in the hepatitis delta virus ribozyme from molecular simulation and 3D-RISM.RNA (New York, N.Y.) · 2015Article
- DFT investigations of phosphotriesters hydrolysis in aqueous solution: a model for DNA single strand scission induced by N-nitrosoureas.Journal of molecular modeling · 2013Article
- Why nature really chose phosphate.Quarterly reviews of biophysics · 2013Review
- Novel insights of structure-based modeling for RNA-targeted drug discovery.Journal of chemical information and modeling · 2012Article
- Accurate proton affinity and gas-phase basicity values for molecules important in biocatalysis.The journal of physical chemistry. B · 2010Article
- Solvent structure and hammerhead ribozyme catalysis.Chemistry & biology · 2008Article
- Role of Mg2+ in hammerhead ribozyme catalysis from molecular simulation.Journal of the American Chemical Society · 2008Article
- Insight into the role of Mg in hammerhead ribozyme catalysis from X-ray crystallography and molecular dynamics simulation.Journal of chemical theory and computation · 2007Article
- CHARMM force field parameters for simulation of reactive intermediates in native and thio-substituted ribozymes.Journal of computational chemistry · 2007Article
Corrections and comments
- Erratum issued
Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Divalent Mg(2+) ions often serve as cofactors in enzyme or ribozyme-catalyzed phosphoryl transfer reactions. In this work, the interaction of Mg(2+) ions and di-metal bridge complexes with phosphates, phosphoranes, and other biological ligands relevant to RNA catalysis are characterized with density functional methods. The effect of bulk solvent is treated with two continuum solvation methods (PCM and COSMO) for comparison. The relative binding affinity for different biological ligands to Mg(2+) are quantified in different protonation states. The structure and stability of the single-metal and di-metal complexes are characterized, and the changes in phosphate and phosphorane geometry induced by metal ion binding are discussed. Di-metal bridge complexes are a ubiquitous motif and the key factors governing their electrostatic stabilization are outlined. The results presented here provide quantitative characterization of metal ion binding to ligands of importance to RNA catalysis, and lay the groundwork for design of new generation quantum models that can be applied to the full biological enzymatic systems.
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