1uhx

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[[Image:1uhx.gif|left|200px]]
 
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==Crystal structure of d(GCGAGAGC): the base-intercalated duplex==
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The line below this paragraph, containing "STRUCTURE_1uhx", creates the "Structure Box" on the page.
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<StructureSection load='1uhx' size='340' side='right'caption='[[1uhx]], [[Resolution|resolution]] 2.00&Aring;' 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'>[[1uhx]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHX OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1UHX 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]] 2&#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=CBR:5-BROMO-2-DEOXY-CYTIDINE-5-MONOPHOSPHATE'>CBR</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NA:SODIUM+ION'>NA</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</scene></td></tr>
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{{STRUCTURE_1uhx| PDB=1uhx | SCENE= }}
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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=1uhx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1uhx OCA], [https://pdbe.org/1uhx PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1uhx RCSB], [https://www.ebi.ac.uk/pdbsum/1uhx PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1uhx ProSAT]</span></td></tr>
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</table>
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'''Crystal structure of d(GCGAGAGC): the base-intercalated duplex'''
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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==Overview==
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DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.
DNA fragments containing the sequence d(GCGAAAGC) prefer to adopt a base-intercalated (zipper-like) duplex in the crystalline state. To investigate effects of point mutation at the 5th residue on the structure, two crystal structures of d(GCGAGAGC) and d(GCGATAGC) have been determined by X-ray crystallography. In the respective crystals, the two octamers related by a crystallographic two-fold symmetry are aligned in an anti-parallel fashion and associated to each other to form a duplex, suggesting that the base-intercalated duplex is stable even when the 5th residue is mutated with other bases. The sheared G3:A6 pair formation makes the two phosphate backbones closer and facilitates formation of the A-X*-X-A* base-intercalated motif. The three duplexes are assembled around the three-fold axis, and their 3rd and 4th residues are bound to the hexamine cobalt chloride. The central 5th residues are bound to another cation.
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==About this Structure==
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X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue.,Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:14646150<ref>PMID:14646150</ref>
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Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1UHX 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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X-ray analyses of d(GCGAXAGC) containing G and T at X: the base-intercalated duplex is still stable even in point mutants at the fifth residue., Kondo J, Umeda S, Fujita K, Sunami T, Takenaka A, J Synchrotron Radiat. 2004 Jan 1;11(Pt 1):117-20. Epub 2003 Nov 28. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/14646150 14646150]
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</div>
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[[Category: Fujita, K.]]
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<div class="pdbe-citations 1uhx" style="background-color:#fffaf0;"></div>
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[[Category: Kondo, J.]]
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== References ==
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[[Category: Sunami, T.]]
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<references/>
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[[Category: Takenaka, A.]]
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__TOC__
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[[Category: Umeda, S I.]]
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</StructureSection>
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[[Category: Base-intercalated duplex]]
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[[Category: Large Structures]]
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[[Category: Base-intercalated motif]]
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[[Category: Fujita K]]
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[[Category: Deoxyribonucleic acid]]
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[[Category: Kondo J]]
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[[Category: Dna]]
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[[Category: Sunami T]]
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[[Category: Sheared g:a pair]]
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[[Category: Takenaka A]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 11:15:27 2008''
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[[Category: Umeda SI]]

Current revision

Crystal structure of d(GCGAGAGC): the base-intercalated duplex

PDB ID 1uhx

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