1rde

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{{Seed}}
 
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[[Image:1rde.png|left|200px]]
 
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==NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+==
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The line below this paragraph, containing "STRUCTURE_1rde", creates the "Structure Box" on the page.
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<StructureSection load='1rde' size='340' side='right'caption='[[1rde]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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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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or leave the SCENE parameter empty for the default display.
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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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{{STRUCTURE_1rde| PDB=1rde | SCENE= }}
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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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===NMR structure of the thrombin-binding DNA aptamer stabilized by Sr2+===
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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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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_15214802}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 1rde" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 15214802 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_15214802}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1RDE OCA].
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[[Category: Gmeiner WH]]
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[[Category: Mao X]]
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==Reference==
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[[Category: Marky LA]]
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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://www.ncbi.nlm.nih.gov/pubmed/15214802 15214802]
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[[Category: Gmeiner, W H.]]
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[[Category: Mao, X.]]
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[[Category: Marky, L A.]]
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[[Category: Quadruplex]]
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[[Category: Sr2+]]
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[[Category: Thrombin-binding dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jul 28 12:38:12 2008''
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Current revision

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

PDB ID 1rde

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