1OMK

The Crystal Structure of d(CACG(5IU)G)

Summary for 1OMK

• Entry DOI: 10.2210/pdb1omk/pdb
• Descriptor: 5'-D(*CP*AP*CP*GP*(5IU)P*G)-3', COBALT HEXAMMINE(III) (3 entities in total)
• Functional Keywords: z-dna, 5-iodo-2'-deoxyuridine, dna
• Total number of polymer chains: 2
• Total formula weight: 4164.41

Authors

Schuerman, G.,Van Hecke, K.,Van Meervelt, L. (deposition date: 2003-02-25, release date: 2003-11-04, Last modification date: 2024-04-03)

Primary citation

Schuerman, G.,Van Hecke, K.,Van Meervelt, L.
Exploration of the influence of 5-iodo-2'-deoxyuridine incorporation on the structure of d[CACG(IDU)G].
Acta Crystallogr.,Sect.D, 59:1525-1528, 2003

PubMed Abstract: 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.

PubMed: 12876373
DOI: 10.1107/S0907444903012381

Experimental method

X-RAY DIFFRACTION (1.3 Å)