PDBsum entry 331d

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NCO ×2
Waters ×57
PDB id:
Name: DNA
Title: Crystal structure of d(gcgcgcg) with 5'-overhang g's
Structure: DNA (5'-d( Gp Cp Gp Cp Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes
1.65Å     R-factor:   0.184    
Authors: B.Pan,C.Ban,M.Wahl,M.Sundaralingam
Key ref: B.Pan et al. (1997). Crystal structure of d(GCGCGCG) with 5'-overhang G residues. Biophys J, 73, 1553-1561. PubMed id: 9284322
13-May-97     Release date:   24-Sep-97    


Biophys J 73:1553-1561 (1997)
PubMed id: 9284322  
Crystal structure of d(GCGCGCG) with 5'-overhang G residues.
B.Pan, C.Ban, M.C.Wahl, M.Sundaralingam.
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.

Literature references that cite this PDB file's key reference

  PubMed id Reference
12595699 B.Pan, and M.Sundaralingam (2003).
Crystal structure of rGd(CGCGCG): a Z-DNA hexamer duplex with a 5'-(rG) overhang.
  Acta Crystallogr D Biol Crystallogr, 59, 433-437.
PDB code: 1m6r
12595546 K.Shi, B.Pan, and M.Sundaralingam (2003).
The crystal structure of an alternating RNA heptamer r(GUAUACA) forming a six base-paired duplex with 3'-end adenine overhangs.
  Nucleic Acids Res, 31, 1392-1397.
PDB code: 1l3z
9687367 W.Shepard, W.B.Cruse, R.Fourme, la Fortelle, and T.Prangé (1998).
A zipper-like duplex in DNA: the crystal structure of d(GCGAAAGCT) at 2.1 A resolution.
  Structure, 6, 849-861.
PDB code: 376d
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