331D | pdb_0000331d

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

• PDB DOI: https://doi.org/10.2210/pdb331D/pdb
• NAKB: 331D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1997-05-13 Released: 1997-09-24 
• Deposition Author(s): Pan, B., Ban, C., Wahl, M., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Work: 
  0.184 (Depositor) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of d(GCGCGCG) with 5'-overhang G residues.

Pan, B., Ban, C., Wahl, M.C., Sundaralingam, M.

(1997) Biophys J 73: 1553-1561

• PubMed: 9284322 
• DOI: https://doi.org/10.1016/S0006-3495(97)78187-6
• Primary Citation Related Structures: 
  331D


• 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.

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Organizational Affiliation: 
• Biological Macromolecular Structure Center, Department of Chemistry, The Ohio State University, Columbus 43210-1002, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 4.6 kDa 
• Atom Count: 355 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*GP*CP*GP*CP*G)-3')	A, B	7	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth A], D [auth A]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Work:  0.184 (Depositor) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 20.41	α = 90
b = 29.65	β = 90
c = 51.86	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
RIGAKU	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1997-09-24 
Deposition Author(s): Pan, B., Ban, C., Wahl, M., Sundaralingam, M.

Revision History  

• Version 1.0: 1997-09-24
  Type: Initial release
  
• Version 1.1: 2008-05-22
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description