3n4n

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{{STRUCTURE_3n4n| PDB=3n4n | SCENE= }}
 
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===Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one===
 
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{{ABSTRACT_PUBMED_20554855}}
 
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==About this Structure==
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==Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one==
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[[3n4n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N4N OCA].
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<StructureSection load='3n4n' size='340' side='right'caption='[[3n4n]], [[Resolution|resolution]] 1.92&Aring;' scene=''>
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== Structural highlights ==
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<table><tr><td colspan='2'>[[3n4n]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3N4N OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3N4N 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">X-ray diffraction, [[Resolution|Resolution]] 1.92&#8491;</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B7C:3-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-7,8-DIHYDROPYRIDO[2,3-D]PYRIMIDIN-2(3H)-ONE'>B7C</scene></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=3n4n FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3n4n OCA], [https://pdbe.org/3n4n PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3n4n RCSB], [https://www.ebi.ac.uk/pdbsum/3n4n PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3n4n 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 incorporation of the bicyclic cytosine analogue 7,8-dihydropyrido[2,3-d]pyrimidin-2-one (X) into DNA duplexes results in a significant enhancement of their stability (3-4 K per modification). To establish the effects of X on the local hydrogen-bonding and base stacking interactions and the overall DNA conformation, and to obtain insights into the correlation between the structure and stability of X-containing DNA duplexes, the crystal structures of [d(CGCGAATT-X-GCG)](2) and [d(CGCGAAT-X-CGCG)](2) have been determined at 1.9-2.9 A resolutions. In all of the structures, the analogue X base pairs with the purine bases on the opposite strands through Watson-Crick and/or wobble type hydrogen bonds. The additional ring of the X base is stacked on the thymine bases at the 5'-side and overall exhibits greatly enhanced stacking interactions suggesting that this is a major contribution to duplex stabilization.
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==Reference==
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Insights into the DNA stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido [2,3-d]pyrimidin-2-one.,Magat Juan EC, Shimizu S, Ma X, Kurose T, Haraguchi T, Zhang F, Tsunoda M, Ohkubo A, Sekine M, Shibata T, Millington CL, Williams DM, Takenaka A Nucleic Acids Res. 2010 Jun 16. PMID:20554855<ref>PMID:20554855</ref>
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<ref group="xtra">PMID:020554855</ref><references group="xtra"/><references/>
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[[Category: Juan, E C.M.]]
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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[[Category: Shimizu, S.]]
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</div>
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[[Category: Takenaka, A.]]
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<div class="pdbe-citations 3n4n" style="background-color:#fffaf0;"></div>
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[[Category: Bicyclic cytosine]]
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== References ==
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[[Category: Dna]]
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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: Juan ECM]]
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[[Category: Shimizu S]]
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[[Category: Takenaka A]]

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Insights into the stabilizing contributions of a bicyclic cytosine analogue: crystal structures of DNA duplexes containing 7,8-dihydropyrido[2,3-d]pyrimidin-2-one

PDB ID 3n4n

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