1ixj: Difference between revisions
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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== | |||
<StructureSection load='1ixj' size='340' side='right'caption='[[1ixj]], [[Resolution|resolution]] 2.50Å' scene=''> | |||
== Structural highlights == | |||
<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> | |||
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.5Å</td></tr> | |||
<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> | |||
<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> | |||
</table> | |||
<div style="background-color:#fffaf0;"> | |||
== Publication Abstract from PubMed == | |||
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. | |||
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> | |||
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | |||
</div> | |||
== | <div class="pdbe-citations 1ixj" style="background-color:#fffaf0;"></div> | ||
[[ | == References == | ||
[[Category: Hirao | <references/> | ||
[[Category: Kobuna | __TOC__ | ||
[[Category: Kondo | </StructureSection> | ||
[[Category: Miura | [[Category: Large Structures]] | ||
[[Category: Sunami | [[Category: Hirao I]] | ||
[[Category: Takenaka | [[Category: Kobuna T]] | ||
[[Category: Watanabe | [[Category: Kondo J]] | ||
[[Category: Miura K]] | |||
[[Category: Sunami T]] | |||
[[Category: Takenaka A]] | |||
[[Category: Watanabe K]] | |||
Latest revision as of 23:38, 27 December 2023
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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