1bd1
From Proteopedia
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CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA
Overview
The DNA decamer d(CCAGGCCTGG) has been studied by X-ray crystallography., At a nominal resolution of 1.6 A, the structure was refined to R = 16.9%, using stereochemical restraints. The oligodeoxyribonucleotide forms a, straight B-DNA double helix with crystallographic dyad symmetry and ten, base-pairs per turn. In the crystal lattice, DNA fragments stack, end-to-end along the c-axis to form continuous double helices. The overall, helical structure and, notably, the groove dimensions of the decamer are, more similar to standard, fiber diffraction-determined B-DNA than A-tract, DNA. A unique stacking geometry is observed at the CA/TG base-pair step, where an increased rotation about the helix axis and a sliding motion of, the base-pairs along their long axes leads to a superposition of the base, rings with neighboring carbonyl and amino functions. Three-center, (bifurcated) hydrogen bonds are possible at the CC/GG base-pair steps of, the decamer. In their common sequence elements, d(CCAGGCCTGG) and the, related G.A mismatch decamer d(CCAAGATTGG) show very similar, three-dimensional structures, except that d(CCAGGCCTGG) appears to have a, less regularly hydrated minor groove. The paucity of minor groove, hydration in the center of the decamer may be a general feature of, G/C-rich DNA and explain its relative instability in the B-form of DNA.
About this Structure
1BD1 is a Protein complex structure of sequences from [1] with TEA as ligand. Full crystallographic information is available from OCA.
Reference
Crystallographic study of one turn of G/C-rich B-DNA., Heinemann U, Alings C, J Mol Biol. 1989 Nov 20;210(2):369-81. PMID:2600970
Page seeded by OCA on Sun Nov 25 00:01:58 2007
