1omk
From Proteopedia
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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] with NCO as ligand. 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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