1D53

CRYSTAL STRUCTURE AT 1.5 ANGSTROMS RESOLUTION OF D(CGCICICG), AN OCTANUCLEOTIDE CONTAINING INOSINE, AND ITS COMPARISON WITH D(CGCG) AND D(CGCGCG) STRUCTURES

Summary for 1D53

• Entry DOI: 10.2210/pdb1d53/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*IP*CP*IP*CP*G)-3'), DNA (5'-D(*CP*GP*CP*G)-3') (3 entities in total)
• Functional Keywords: z-dna, double helix, dna
• Total number of polymer chains: 4
• Total formula weight: 3530.50

Authors

Kumar, V.D.,Harrison, R.W.,Andrews, L.C.,Weber, I.T. (deposition date: 1992-11-05, release date: 1993-04-13, Last modification date: 2024-02-07)

Primary citation

Kumar, V.D.,Harrison, R.W.,Andrews, L.C.,Weber, I.T.
Crystal structure at 1.5-A resolution of d(CGCICICG), an octanucleotide containing inosine, and its comparison with d(CGCG) and d(CGCGCG) structures.
Biochemistry, 31:1541-1550, 1992

PubMed Abstract: The octadeoxyribonucleotide d(CGCICICG) has been crystallized in space group P(6)5(22) with unit cell dimensions of a = b = 31.0 A and c = 43.7 A, and X-ray diffraction data have been collected to 1.5-A resolution. Precession photographs and the self-Patterson function indicate that 12 base pairs of Z-conformation DNA stack along the c-axis, and the double helices pack in a hexagonal array similar to that seen in other crystals of Z-DNA. The structure has been solved by both Patterson deconvolution and molecular replacement methods and refined in space group P(6)5 to an R factor of 0.225 using 2503 unique reflections greater than 3.0 sigma (F). Comparison of the molecules within the hexagonal lattice with highly refined crystal structures of other Z-DNA reveals only minor conformational differences, most notably in the pucker of the deoxyribose of the purine residues. The DNA has multiple occupancy of C:I and C:G base pairs, and C:I base pairs adopt a conformation similar to that of C:G base pairs.

PubMed: 1737011
DOI: 10.1021/bi00120a035

Experimental method

X-RAY DIFFRACTION (1.5 Å)