331D

CRYSTAL STRUCTURE OF D(GCGCGCG) WITH 5'-OVERHANG G'S

Summary for 331D

• Entry DOI: 10.2210/pdb331d/pdb
• Descriptor: DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3'), COBALT HEXAMMINE(III) (3 entities in total)
• Functional Keywords: z-dna, double helix, overhanging base, flipped-out base, dna
• Total number of polymer chains: 2
• Total formula weight: 4601.05

Authors

Pan, B.,Ban, C.,Wahl, M.,Sundaralingam, M. (deposition date: 1997-05-13, release date: 1997-09-24, Last modification date: 2024-04-03)

Primary citation

Pan, B.,Ban, C.,Wahl, M.C.,Sundaralingam, M.
Crystal structure of d(GCGCGCG) with 5'-overhang G residues.
Biophys.J., 73:1553-1561, 1997

PubMed Abstract: The crystal structure of the DNA heptamer d(GCGCGCG) has been solved at 1.65 A resolution by the molecular replacement method and refined to an R-value of 0.184 for 3598 reflections. The heptamer forms a Z-DNA d(CGCGCG)2 with 5'-overhang G residues instead of an A-DNA d(GCGCGC)2 with 3'-overhang G residues. The overhang G residues from parallel strands of two adjacent duplexes form a trans reverse Hoogsteen G x G basepair that stacks on the six Z-DNA basepairs to produce a pseudocontinuous helix. The reverse Hoogsteen G x G basepair is unusual in that the displacement of one G base relative to the other allows them to participate in a bifurcated (G1)N2 . . . N7(G8) and an enhanced (G8)C8-H . . . O6(G1) hydrogen bond, in addition to the two usual hydrogen bonds. The 5'-overhang G residues are anti and C2'-endo while the 3'-terminal G residues are syn and C2'-endo. The conformations of both G residues are different from the syn/C3'-endo for the guanosine in a standard Z-DNA. The two cobalt hexammine ions bind to the phosphate groups in both GpC and CpG steps in Z(I) and Z(II) conformations. The water structure motif is similar to the other Z-DNA structures.

PubMed: 9284322

Experimental method

X-RAY DIFFRACTION (1.65 Å)