1BD1

CRYSTALLOGRAPHIC STUDY OF ONE TURN OF G/C-RICH B-DNA

Summary for 1BD1

• Entry DOI: 10.2210/pdb1bd1/pdb
• Descriptor: DNA (5'-D(*CP*CP*AP*GP*GP*CP*CP*TP*GP*G)-3'), TRIETHYLAMMONIUM ION (3 entities in total)
• Functional Keywords: b-dna, double helix, dna
• Total number of polymer chains: 1
• Total formula weight: 3250.39

Authors

Heinemann, U. (deposition date: 1989-08-16, release date: 1990-01-15, Last modification date: 2024-02-07)

Primary citation

Heinemann, U.,Alings, C.
Crystallographic study of one turn of G/C-rich B-DNA.
J.Mol.Biol., 210:369-381, 1989

PubMed Abstract: 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.

PubMed: 2600970
DOI: 10.1016/0022-2836(89)90337-9

Experimental method

X-RAY DIFFRACTION (1.6 Å)