210D | pdb_0000210d

CRYSTAL AND MOLECULAR STRUCTURE OF A NEW Z-DNA CRYSTAL FORM: D[CGT(2-NH2-A)CG] AND ITS PLATINATED DERIVATIVE

• PDB DOI: https://doi.org/10.2210/pdb210D/pdb
• NAKB: 210D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1995-06-13 Released: 1996-03-22 
• Deposition Author(s): Parkinson, G.N., Arvantis, G.M., Lessinger, L., Ginell, S.L., Jones, R., Gaffney, B., Berman, H.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Work: 
  0.174 (Depositor), 0.283 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Literature

Crystal and molecular structure of a new Z-DNA crystal form: d[CGT(2-NH2-A)CG] and its platinated derivative.

Parkinson, G.N., Arvanitis, G.M., Lessinger, L., Ginell, S.L., Jones, R., Gaffney, B., Berman, H.M.

(1995) Biochemistry 34: 15487-15495

• PubMed: 7492550 
• DOI: https://doi.org/10.1021/bi00047a014
• Primary Citation Related Structures: 
  210D, 211D


• PubMed Abstract: 
  

  The three-dimensional structure of d[CGTA'CG], where A' = [2-NH2-A], was determined to atomic (1.35 A) resolution by single isomorphous replacement. The d[CGTA'CG] hexamer crystallizes in space group P3221, and is not isomorphous with other DNA hexanucleotides. Despite completely different crystal packing, the essential characteristics of the Z-DNA conformation are maintained. The structure was determined by single isomorphous replacement using a triammine platinum fragment. Thus, this study also demonstrates, for the first time, the feasibility of the use of this reagent for the direct phasing of DNA crystal structures.

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Organizational Affiliation: 
• Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855-0939, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 2.03 kDa 
• Atom Count: 162 
• Modeled Residue Count: 6 
• Deposited Residue Count: 6 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*TP*(1AP)P*CP*G)-3')	A	6	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	B [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Work:  0.174 (Depositor), 0.283 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.247	α = 90
b = 25.247	β = 90
c = 39.14	γ = 120

Software Package:

Software Name	Purpose
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-03-22 
Deposition Author(s): Parkinson, G.N., Arvantis, G.M., Lessinger, L., Ginell, S.L., Jones, R., Gaffney, B., Berman, H.M.

Revision History  

• Version 1.0: 1996-03-22
  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: 2018-04-18
  Changes: Data collection
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references, Derived calculations