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New page: left|200px<br /><applet load="232d" size="350" color="white" frame="true" align="right" spinBox="true" caption="232d, resolution 1.300Å" /> '''THE HIGH RESOLUTION...
 
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[[Image:232d.gif|left|200px]]<br /><applet load="232d" size="350" color="white" frame="true" align="right" spinBox="true"
caption="232d, resolution 1.300&Aring;" />
'''THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT)'''<br />


==Overview==
==THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT)==
The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined, to a resolution of 1.3 A and R factor of 13.9%. The structure has a unique, conformation with each of the decamer single strands forming base-pairing, interactions with two symmetry-related strands. The central eight bases of, the decamer form an A-DNA octamer duplex with one symmetry-related strand, whilst the terminal 5'-A and T-3' bases are flipped out and away from the, octamer helix axis to form base-pairing interactions with a second, symmetry-related strand. These A.T base-pairs lie perpendicular to the, crystallographic c axis and pack within the unit cell in conjunction with, a symmetry-related A.T base-pair displaced by 3.4 A degrees along the c, axis. A novel base triplet interaction of the type A*(G.C) is present in, the structure with interaction from the major groove side of the terminal, 5'-A base to the minor groove of the central A-DNA octamer. This structure, reports the first example of cobalt hexammine binding to a right-handed, DNA duplex. The crystallographic asymmetric unit contains two cobalt, hexammine ligands with one site in the major groove coordinating via, hydrogen bonds to the 5'-AGG bases, and the second site located between, DNA molecules and interacting with the oxygen atoms of phosphate groups.
<StructureSection load='232d' size='340' side='right'caption='[[232d]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[232d]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=232D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=232D 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]] 1.3&#8491;</td></tr>
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><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=232d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=232d OCA], [https://pdbe.org/232d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=232d RCSB], [https://www.ebi.ac.uk/pdbsum/232d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=232d ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The crystal structure of the DNA decamer d(AGGCATGCCT) has been determined to a resolution of 1.3 A and R factor of 13.9%. The structure has a unique conformation with each of the decamer single strands forming base-pairing interactions with two symmetry-related strands. The central eight bases of the decamer form an A-DNA octamer duplex with one symmetry-related strand whilst the terminal 5'-A and T-3' bases are flipped out and away from the octamer helix axis to form base-pairing interactions with a second symmetry-related strand. These A.T base-pairs lie perpendicular to the crystallographic c axis and pack within the unit cell in conjunction with a symmetry-related A.T base-pair displaced by 3.4 A degrees along the c axis. A novel base triplet interaction of the type A*(G.C) is present in the structure with interaction from the major groove side of the terminal 5'-A base to the minor groove of the central A-DNA octamer. This structure reports the first example of cobalt hexammine binding to a right-handed DNA duplex. The crystallographic asymmetric unit contains two cobalt hexammine ligands with one site in the major groove coordinating via hydrogen bonds to the 5'-AGG bases, and the second site located between DNA molecules and interacting with the oxygen atoms of phosphate groups.


==About this Structure==
The high resolution crystal structure of the DNA decamer d(AGGCATGCCT).,Nunn CM, Neidle S J Mol Biol. 1996 Feb 23;256(2):340-51. PMID:8594201<ref>PMID:8594201</ref>
232D is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=NCO:'>NCO</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=232D OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
The high resolution crystal structure of the DNA decamer d(AGGCATGCCT)., Nunn CM, Neidle S, J Mol Biol. 1996 Feb 23;256(2):340-51. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=8594201 8594201]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 232d" style="background-color:#fffaf0;"></div>
[[Category: Neidle, S.]]
== References ==
[[Category: Nunn, C.M.]]
<references/>
[[Category: NCO]]
__TOC__
[[Category: a-dna]]
</StructureSection>
[[Category: double helix]]
[[Category: Large Structures]]
[[Category: flipped-out bases]]
[[Category: Neidle S]]
 
[[Category: Nunn CM]]
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jan 29 17:48:15 2008''

Latest revision as of 07:43, 13 August 2026

THE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGGCATGCCT)

232d, resolution 1.30Å

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