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| | ==Refined NMR solution structure of metal-modified DNA== | | ==Refined NMR solution structure of metal-modified DNA== |
| - | <StructureSection load='2m54' size='340' side='right' caption='[[2m54]], [[NMR_Ensembles_of_Models | 20 NMR models]]' scene=''> | + | <StructureSection load='2m54' size='340' side='right'caption='[[2m54]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[2m54]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M54 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2M54 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[2m54]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2M54 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2M54 FirstGlance]. <br> |
| - | </td></tr><tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat"><scene name='pdbligand=AG:SILVER+ION'>AG</scene></td></tr> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr> |
| - | <tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><scene name='pdbligand=D33:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-IMIDAZOLE'>D33</scene></td></tr> | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AG:SILVER+ION'>AG</scene>, <scene name='pdbligand=D33:1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-1H-IMIDAZOLE'>D33</scene></td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[2ke8|2ke8]], [[2k68|2k68]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2m54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m54 OCA], [https://pdbe.org/2m54 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2m54 RCSB], [https://www.ebi.ac.uk/pdbsum/2m54 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2m54 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=2m54 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2m54 OCA], [http://pdbe.org/2m54 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=2m54 RCSB], [http://www.ebi.ac.uk/pdbsum/2m54 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=2m54 ProSAT]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Johannsen, S]] | + | [[Category: Large Structures]] |
| - | [[Category: Kumbhar, S]] | + | [[Category: Johannsen S]] |
| - | [[Category: Mueller, J]] | + | [[Category: Kumbhar S]] |
| - | [[Category: Sigel, R K]] | + | [[Category: Mueller J]] |
| - | [[Category: Waller, M P]] | + | [[Category: Sigel RK]] |
| - | [[Category: Artificial nucleobase]]
| + | [[Category: Waller MP]] |
| - | [[Category: Dna]]
| + | |
| - | [[Category: Imidazole nucleoside]]
| + | |
| Structural highlights
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[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Kumbhar S, Johannsen S, Sigel RK, Waller MP, Muller J. A QM/MM refinement of an experimental DNA structure with metal-mediated base pairs. J Inorg Biochem. 2013 Mar 28. pii: S0162-0134(13)00067-6. doi:, 10.1016/j.jinorgbio.2013.03.009. PMID:23622950 doi:10.1016/j.jinorgbio.2013.03.009
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