2m54 | pdb_00002m54

Refined NMR solution structure of metal-modified DNA

spinqualitylabelsall models 2m54 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 2m54 is a 2 chain structure. Full experimental information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: Solution NMR Ligands: AG, D33 Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed A series of hybrid quantum mechanical/molecular mechanical (QM/MM) calculations was performed on models of a DNA duplex with artificial silver(I)-mediated imidazole base pairs. The optimized structures were compared to the original experimental NMR structure (Nat. Chem. 2 (2010) 229-234). The metalcdots, three dots, centeredmetal distances are significantly shorter (~0.5A) in the QM/MM model than in the original NMR structure. As a result, argentophilic interactions are feasible between the silver(I) ions of neighboring metal-mediated base pairs. Using the computationally determined metalcdots, three dots, centeredmetal distances, a re-refined NMR solution structure of the DNA duplex was obtained. In this new NMR structure, all experimental constraints remain fulfilled. The new NMR structure shows less deviation from the regular B-type conformation than the original one. This investigation shows that the application of QM/MM models to generate additional constraints to be used during NMR structural refinements represents an elegant approach to obtaining high-resolution NMR structures. A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs.,Kumbhar S, Johannsen S, Sigel RK, Waller MP, Muller J J Inorg Biochem. 2013 Mar 28. pii: S0162-0134(13)00067-6. doi:, 10.1016/j.jinorgbio.2013.03.009. PMID:23622950 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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