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New page: left|200px<br /><applet load="1omk" size="450" color="white" frame="true" align="right" spinBox="true" caption="1omk, resolution 1.30Å" /> '''The Crystal Structur...
 
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[[Image:1omk.gif|left|200px]]<br /><applet load="1omk" size="450" color="white" frame="true" align="right" spinBox="true"
caption="1omk, resolution 1.30&Aring;" />
'''The Crystal Structure of d(CACG(5IU)G)'''<br />


==Overview==
==The Crystal Structure of d(CACG(5IU)G)==
The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes, simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5, methyl group is replaced by an I atom. The structure of the, self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal, X-ray diffraction techniques. The orthorhombic crystals belong to space, group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c =, 41.99 A. Refinement in the resolution range 20-1.3 A converged with a, final R1 = 0.167, including 43 water molecules and two cobalt hexammine, complexes. The incorporation of a large I atom has only minor consequences, for the overall structure as is noticed in the IDU.A base pairs, which are, of the common Watson-Crick type. To contribute to the still puzzling, mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of, cobalt hexammine-binding modes in Z-DNA is provided, revealing similar, binding modes for the reported structure.
<StructureSection load='1omk' size='340' side='right'caption='[[1omk]], [[Resolution|resolution]] 1.30&Aring;' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1omk]] is a 2 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1OMK OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1OMK 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=5IU:5-IODO-2-DEOXYURIDINE-5-MONOPHOSPHATE'>5IU</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=1omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omk OCA], [https://pdbe.org/1omk PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1omk RCSB], [https://www.ebi.ac.uk/pdbsum/1omk PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1omk ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The first antiviral nucleoside 5-iodo-2'-deoxyuridine (IDU) against herpes simplex virus type 1 and type 2 is a thymidine analogue, i.e. the C5 methyl group is replaced by an I atom. The structure of the self-complementary hexamer d[CACG(IDU)G] was determined by single-crystal X-ray diffraction techniques. The orthorhombic crystals belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 18.16, b = 30.03, c = 41.99 A. Refinement in the resolution range 20-1.3 A converged with a final R1 = 0.167, including 43 water molecules and two cobalt hexammine complexes. The incorporation of a large I atom has only minor consequences for the overall structure as is noticed in the IDU.A base pairs, which are of the common Watson-Crick type. To contribute to the still puzzling mechanism of this historically important agent, details of base stacking, helical parameters, hydration etc. have been studied. A general scheme of cobalt hexammine-binding modes in Z-DNA is provided, revealing similar binding modes for the reported structure.


==About this Structure==
Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G].,Schuerman G, Van Hecke K, Van Meervelt L Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1525-8. Epub 2003, Jul 23. PMID:12876373<ref>PMID:12876373</ref>
1OMK is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with NCO as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://ispc.weizmann.ac.il/oca-bin/ocashort?id=1OMK OCA].


==Reference==
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G]., Schuerman G, Van Hecke K, Van Meervelt L, Acta Crystallogr D Biol Crystallogr. 2003 Aug;59(Pt 8):1525-8. Epub 2003, Jul 23. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=12876373 12876373]
</div>
[[Category: Protein complex]]
<div class="pdbe-citations 1omk" style="background-color:#fffaf0;"></div>
[[Category: Hecke, K.Van.]]
== References ==
[[Category: Meervelt, L.Van.]]
<references/>
[[Category: Schuerman, G.]]
__TOC__
[[Category: NCO]]
</StructureSection>
[[Category: 5-iodo-2'-deoxyuridine]]
[[Category: Large Structures]]
[[Category: z-dna]]
[[Category: Schuerman G]]
 
[[Category: Van Hecke K]]
''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sun Nov 25 01:06:36 2007''
[[Category: Van Meervelt L]]
Retrieved from "https://proteopedia.org/1omk"