1rde

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(New page: 200px<br /><applet load="1rde" size="450" color="white" frame="true" align="right" spinBox="true" caption="1rde" /> '''NMR structure of the thrombin-binding DNA ap...)
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[[Image:1rde.gif|left|200px]]<br /><applet load="1rde" size="450" color="white" frame="true" align="right" spinBox="true"
 
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caption="1rde" />
 
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'''NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+'''<br />
 
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==Overview==
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==NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+==
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The structure of thrombin-binding DNA aptamer complexed with a single Sr2+, ion (Sr2+:TBA complex) has been determined using NMR spectroscopy and, restrained molecular dynamics simulations. The quadruplex structure for, the Sr2+:TBA complex is similar in topology, but distinct in structure, from that previously reported for the K+:TBA complex. The inter-tetrad, distance of the Sr2+:TBA complex is 3.8 angstroms, or 0.7 angstroms larger, than in the K+:TBA complex. This substantial difference can be attributed, to a different binding site for Sr2+ in the Sr2+:TBA complex than for K+, in the K+:TBA complex. The Sr2+:TBA complex assumes a 1:1 stoichiometry, and it is very likely that the Sr2+ ion simultaneously interacts with the, eight O6 atoms of the two G-tetrads. The results indicate that quadruplex, DNA structures are highly sensitive to the presence of specific metal, ions. The binding of specific metal ions may modulate the biological, activity of quadruplex DNA structures in vivo.
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<StructureSection load='1rde' size='340' side='right'caption='[[1rde]]' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[1rde]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDE OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1RDE FirstGlance]. <br>
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1rde FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1rde OCA], [https://pdbe.org/1rde PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1rde RCSB], [https://www.ebi.ac.uk/pdbsum/1rde PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1rde ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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The structure of thrombin-binding DNA aptamer complexed with a single Sr2+ ion (Sr2+:TBA complex) has been determined using NMR spectroscopy and restrained molecular dynamics simulations. The quadruplex structure for the Sr2+:TBA complex is similar in topology, but distinct in structure, from that previously reported for the K+:TBA complex. The inter-tetrad distance of the Sr2+:TBA complex is 3.8 angstroms, or 0.7 angstroms larger than in the K+:TBA complex. This substantial difference can be attributed to a different binding site for Sr2+ in the Sr2+:TBA complex than for K+ in the K+:TBA complex. The Sr2+:TBA complex assumes a 1:1 stoichiometry, and it is very likely that the Sr2+ ion simultaneously interacts with the eight O6 atoms of the two G-tetrads. The results indicate that quadruplex DNA structures are highly sensitive to the presence of specific metal ions. The binding of specific metal ions may modulate the biological activity of quadruplex DNA structures in vivo.
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==About this Structure==
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NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+.,Mao X, Marky LA, Gmeiner WH J Biomol Struct Dyn. 2004 Aug;22(1):25-33. PMID:15214802<ref>PMID:15214802</ref>
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1RDE is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1RDE OCA].
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==Reference==
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+., Mao X, Marky LA, Gmeiner WH, J Biomol Struct Dyn. 2004 Aug;22(1):25-33. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=15214802 15214802]
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</div>
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[[Category: Protein complex]]
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<div class="pdbe-citations 1rde" style="background-color:#fffaf0;"></div>
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[[Category: Gmeiner, W.H.]]
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== References ==
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[[Category: Mao, X.]]
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<references/>
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[[Category: Marky, L.A.]]
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__TOC__
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[[Category: quadruplex]]
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</StructureSection>
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[[Category: sr2+]]
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[[Category: Large Structures]]
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[[Category: thrombin-binding dna]]
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[[Category: Gmeiner WH]]
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[[Category: Mao X]]
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''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 22:32:15 2007''
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[[Category: Marky LA]]

Current revision

NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+

PDB ID 1rde

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