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| - | [[Image:1omk.gif|left|200px]] | |
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| - | {{Structure
| + | ==The Crystal Structure of d(CACG(5IU)G)== |
| - | |PDB= 1omk |SIZE=350|CAPTION= <scene name='initialview01'>1omk</scene>, resolution 1.30Å
| + | <StructureSection load='1omk' size='340' side='right'caption='[[1omk]], [[Resolution|resolution]] 1.30Å' scene=''> |
| - | |SITE=
| + | == Structural highlights == |
| - | |LIGAND= <scene name='pdbligand=5IU:5-IODO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE'>5IU</scene>, <scene name='pdbligand=DA:2'-DEOXYADENOSINE-5'-MONOPHOSPHATE'>DA</scene>, <scene name='pdbligand=DC:2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE'>DC</scene>, <scene name='pdbligand=DG:2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE'>DG</scene>, <scene name='pdbligand=NCO:COBALT+HEXAMMINE+ION'>NCO</scene>
| + | <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> |
| - | |ACTIVITY=
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.3Å</td></tr> |
| - | |GENE=
| + | <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> |
| - | |DOMAIN=
| + | <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> |
| - | |RELATEDENTRY=
| + | </table> |
| - | |RESOURCES=<span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1omk FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1omk OCA], [http://www.ebi.ac.uk/pdbsum/1omk PDBsum], [http://www.rcsb.org/pdb/explore.do?structureId=1omk RCSB]</span>
| + | __TOC__ |
| - | }}
| + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | '''The Crystal Structure of d(CACG(5IU)G)'''
| + | [[Category: Schuerman G]] |
| - | | + | [[Category: Van Hecke K]] |
| - | | + | [[Category: Van Meervelt L]] |
| - | ==Overview==
| + | |
| - | 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.
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| - | | + | |
| - | ==About this Structure==
| + | |
| - | 1OMK 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=1OMK OCA].
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| - | | + | |
| - | ==Reference==
| + | |
| - | 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://www.ncbi.nlm.nih.gov/pubmed/12876373 12876373]
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| - | [[Category: Protein complex]]
| + | |
| - | [[Category: Hecke, K Van.]]
| + | |
| - | [[Category: Meervelt, L Van.]] | + | |
| - | [[Category: Schuerman, G.]] | + | |
| - | [[Category: 5-iodo-2'-deoxyuridine]] | + | |
| - | [[Category: z-dna]] | + | |
| - | | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:47:25 2008''
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