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1ixj

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[[Image:1ixj.gif|left|200px]]
 
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{{Structure
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==Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs==
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|PDB= 1ixj |SIZE=350|CAPTION= <scene name='initialview01'>1ixj</scene>, resolution 2.5&Aring;
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<StructureSection load='1ixj' size='340' side='right'caption='[[1ixj]], [[Resolution|resolution]] 2.50&Aring;' scene=''>
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|SITE=
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== Structural highlights ==
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|LIGAND= <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>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>
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<table><tr><td colspan='2'>[[1ixj]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1IXJ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1IXJ 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">X-ray diffraction, [[Resolution|Resolution]] 2.5&#8491;</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=MG:MAGNESIUM+ION'>MG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE(III)'>NCO</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=1ixj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixj OCA], [https://pdbe.org/1ixj PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ixj RCSB], [https://www.ebi.ac.uk/pdbsum/1ixj PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ixj 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=1ixj FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ixj OCA], [http://www.ebi.ac.uk/pdbsum/1ixj PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1ixj 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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'''Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs'''
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==Overview==
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A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half of the oligomer form a parallel duplex with another half through the homo base pairs, C2:C2+ (singly-protonated between the Watson- Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The two strands remaining in the half of the parallel duplex are split away in different directions, and they pair in an anti-parallel B-form duplex with the second half extending from a neighboring parallel duplex, so that an infinite column is formed in a head-to-tail fashion along the c-axis. It seems that a hexa-ammine cobalt cation supports such a branched and bent conformation of the oligomer. One end of the parallel duplex is stacked on the corresponding end of the adjacent parallel duplex; between them, the guanine base of the first residue is stacked on the fourth ribose of another duplex.
A DNA fragment d(GCGAAAGCT), known to adopt a stable mini-hairpin structure in solution, has been crystallized in the space group I4(1)22 with the unit-cell dimensions a = b = 53.4 A and c = 54.0 A, and the crystal structure has been determined at 2.5 A resolution. The four nucleotide residues CGAA of the first half of the oligomer form a parallel duplex with another half through the homo base pairs, C2:C2+ (singly-protonated between the Watson- Crick sites), G3:G3 (between the minor groove sites), A4:A4 (between the major groove sites) and A5:A5 (between the Watson-Crick sites). The two strands remaining in the half of the parallel duplex are split away in different directions, and they pair in an anti-parallel B-form duplex with the second half extending from a neighboring parallel duplex, so that an infinite column is formed in a head-to-tail fashion along the c-axis. It seems that a hexa-ammine cobalt cation supports such a branched and bent conformation of the oligomer. One end of the parallel duplex is stacked on the corresponding end of the adjacent parallel duplex; between them, the guanine base of the first residue is stacked on the fourth ribose of another duplex.
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==About this Structure==
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Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs.,Sunami T, Kondo J, Kobuna T, Hirao I, Watanabe K, Miura K, Takenaka A Nucleic Acids Res. 2002 Dec 1;30(23):5253-60. PMID:12466550<ref>PMID:12466550</ref>
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1IXJ 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=1IXJ OCA].
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==Reference==
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Crystal structure of d(GCGAAAGCT) containing a parallel-stranded duplex with homo base pairs and an anti-parallel duplex with Watson-Crick base pairs., Sunami T, Kondo J, Kobuna T, Hirao I, Watanabe K, Miura K, Takenaka A, Nucleic Acids Res. 2002 Dec 1;30(23):5253-60. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/12466550 12466550]
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[[Category: Protein complex]]
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[[Category: Hirao, I.]]
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[[Category: Kobuna, T.]]
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[[Category: Kondo, J.]]
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[[Category: Miura, K.]]
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[[Category: Sunami, T.]]
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[[Category: Takenaka, A.]]
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[[Category: Watanabe, K.]]
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[[Category: homo base pair]]
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[[Category: parallel dna]]
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[[Category: parallel duplex]]
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[[Category: parallel-stranded helix]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 21:26:08 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 1ixj" 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: Hirao I]]
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[[Category: Kobuna T]]
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[[Category: Kondo J]]
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[[Category: Miura K]]
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[[Category: Sunami T]]
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[[Category: Takenaka A]]
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[[Category: Watanabe K]]

Current revision

Crystal Structure of d(GCGAAAGCT) Containing Parallel-stranded Duplex with Homo Base Pairs and Anti-Parallel Duplex with Watson-Crick Base pairs

PDB ID 1ixj

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