1old

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[[Image:1old.gif|left|200px]]
 
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{{Structure
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==NMR STRUCTURE OF 24-MER DEOXYRIBONUCLEIC ACID, 7 STRUCTURES==
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|PDB= 1old |SIZE=350|CAPTION= <scene name='initialview01'>1old</scene>
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<StructureSection load='1old' size='340' side='right'caption='[[1old]]' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <scene name='pdbligand=ARM:DEOXY-METHYL-ARGININE'>ARM</scene>, <scene name='pdbligand=DA:2&#39;-DEOXYADENOSINE-5&#39;-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2&#39;-DEOXYCYTIDINE-5&#39;-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2&#39;-DEOXYGUANOSINE-5&#39;-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=DT:THYMIDINE-5&#39;-MONOPHOSPHATE'>DT</scene>
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<table><tr><td colspan='2'>[[1old]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OLD OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OLD FirstGlance]. <br>
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|ACTIVITY=
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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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|GENE=
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=AAR:ARGININEAMIDE'>AAR</scene></td></tr>
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|DOMAIN=
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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=1old FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1old OCA], [https://pdbe.org/1old PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1old RCSB], [https://www.ebi.ac.uk/pdbsum/1old PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1old ProSAT]</span></td></tr>
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|RELATEDENTRY=
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</table>
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|RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1old FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1old OCA], [http://www.ebi.ac.uk/pdbsum/1old PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1old RCSB]</span>
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<div style="background-color:#fffaf0;">
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}}
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== Publication Abstract from PubMed ==
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'''NMR STRUCTURE OF 24-MER DEOXYRIBONUCLEIC ACID, 7 STRUCTURES'''
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==Overview==
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Here we present the first solution structure of a ligand-DNA aptamer complex. Our NMR-molecular dynamics structural studies of the interaction between argininamide and a DNA stem-loop complex establishes that the hairpin loop DNA binding site undergoes an adaptive conformational transition on complex formation. The tip of the DNA loop folds down towards the stem and sandwiches the bound argininamide between reversed Hoogsteen A.C and Watson-Crick G.C base pairs. The argininamide is encapsulated within the structured DNA loop and is stabilized by an intricate set of intermolecular hydrogen bonds and stacking interactions. The structure of the complex lays out the molecular principles defining both the architecture of the internal cavity and the recognition elements that could contribute to ligand discrimination.
Here we present the first solution structure of a ligand-DNA aptamer complex. Our NMR-molecular dynamics structural studies of the interaction between argininamide and a DNA stem-loop complex establishes that the hairpin loop DNA binding site undergoes an adaptive conformational transition on complex formation. The tip of the DNA loop folds down towards the stem and sandwiches the bound argininamide between reversed Hoogsteen A.C and Watson-Crick G.C base pairs. The argininamide is encapsulated within the structured DNA loop and is stabilized by an intricate set of intermolecular hydrogen bonds and stacking interactions. The structure of the complex lays out the molecular principles defining both the architecture of the internal cavity and the recognition elements that could contribute to ligand discrimination.
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==About this Structure==
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Encapsulating an amino acid in a DNA fold.,Lin CH, Patel DJ Nat Struct Biol. 1996 Dec;3(12):1046-50. PMID:8946859<ref>PMID:8946859</ref>
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1OLD is a [[Protein complex]] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OLD OCA].
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==Reference==
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Encapsulating an amino acid in a DNA fold., Lin CH, Patel DJ, Nat Struct Biol. 1996 Dec;3(12):1046-50. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8946859 8946859]
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[[Category: Protein complex]]
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[[Category: Lin, C H.]]
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[[Category: Patel, D J.]]
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[[Category: deoxyribonucleic acid]]
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[[Category: dna]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:46:56 2008''
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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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<div class="pdbe-citations 1old" style="background-color:#fffaf0;"></div>
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== References ==
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<references/>
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__TOC__
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</StructureSection>
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[[Category: Large Structures]]
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[[Category: Lin CH]]
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[[Category: Patel DJ]]

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NMR STRUCTURE OF 24-MER DEOXYRIBONUCLEIC ACID, 7 STRUCTURES

PDB ID 1old

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