3qk4: Difference between revisions
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==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex== | ==Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex== | ||
<StructureSection load='3qk4' size='340' side='right' caption='[[3qk4]], [[Resolution|resolution]] 2.60Å' scene=''> | <StructureSection load='3qk4' size='340' side='right'caption='[[3qk4]], [[Resolution|resolution]] 2.60Å' scene=''> | ||
== Structural highlights == | == Structural highlights == | ||
<table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [ | <table><tr><td colspan='2'>[[3qk4]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=3QK4 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=3QK4 FirstGlance]. <br> | ||
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | </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=3qk4 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=3qk4 OCA], [https://pdbe.org/3qk4 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=3qk4 RCSB], [https://www.ebi.ac.uk/pdbsum/3qk4 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=3qk4 ProSAT]</span></td></tr> | ||
</table> | </table> | ||
<div style="background-color:#fffaf0;"> | <div style="background-color:#fffaf0;"> | ||
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
[[Category: Large Structures]] | |||
[[Category: Gautham, N]] | [[Category: Gautham, N]] | ||
[[Category: Mandal, P K]] | [[Category: Mandal, P K]] | ||
Revision as of 09:12, 8 June 2022
Crystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplexCrystal structure of d(CGCGGGTACCCGCG)2 as A-DNA duplex
Structural highlights
Publication Abstract from PubMedWe report the 2.6A resolution crystal structure of the tetra-decamer d(CGCGGGTACCCGCG) in the tetragonal space group P4(3). This sequence contains the KpnI restriction site GGTACC in the centre which is flanked by alternating 'CG' sequences, and has a 'TA' step at the centre. These are features could favour the left-handed Z type helix. Despite this, overall the molecule has the A form. This is the first tetra-decamer crystallized in the A-DNA conformation, i.e. more than one full turn of the A helix. The crystallographic asymmetric unit consists of one tetra-decamer duplex. The helical twist and slide, as well as the base pair-base pair stacking interactions show alternations at the alternating pyrimidine-purine and purine-pyrimidine base steps. This variation is reminiscent of the dinucleotide repeat in left-handed Z-DNA helices. The crystal packing is unlike other A-DNA crystal structures, with each helix having a large number of contacts of many different types with symmetry-related neighbours. The structure of a full turn of an A-DNA duplex d(CGCGGGTACCCGCG)(2).,Venkadesh S, Mandal PK, Gautham N Biochem Biophys Res Commun. 2011 Apr 8;407(2):307-12. Epub 2011 Mar 21. PMID:21397589[1] From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine. References
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