1omk
From Proteopedia
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|PDB= 1omk |SIZE=350|CAPTION= <scene name='initialview01'>1omk</scene>, resolution 1.30Å | |PDB= 1omk |SIZE=350|CAPTION= <scene name='initialview01'>1omk</scene>, resolution 1.30Å | ||
|SITE= | |SITE= | ||
| - | |LIGAND= <scene name='pdbligand=NCO:COBALT HEXAMMINE ION'>NCO</scene> | + | |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> |
|ACTIVITY= | |ACTIVITY= | ||
|GENE= | |GENE= | ||
| + | |DOMAIN= | ||
| + | |RELATEDENTRY= | ||
| + | |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> | ||
}} | }} | ||
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[[Category: Meervelt, L Van.]] | [[Category: Meervelt, L Van.]] | ||
[[Category: Schuerman, G.]] | [[Category: Schuerman, G.]] | ||
| - | [[Category: NCO]] | ||
[[Category: 5-iodo-2'-deoxyuridine]] | [[Category: 5-iodo-2'-deoxyuridine]] | ||
[[Category: z-dna]] | [[Category: z-dna]] | ||
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun Mar 30 22:47:25 2008'' |
Revision as of 19:47, 30 March 2008
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| , resolution 1.30Å | |||||||
|---|---|---|---|---|---|---|---|
| Ligands: | , , , , | ||||||
| Resources: | FirstGlance, OCA, PDBsum, RCSB | ||||||
| Coordinates: | save as pdb, mmCIF, xml | ||||||
The Crystal Structure of d(CACG(5IU)G)
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.
About this Structure
1OMK is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
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:12876373
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