211D

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1021/bi00047a014
  • Structures With Same Primary Citation

  • 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 hexan ...

    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.


    Organizational Affiliation

    Department of Chemistry, Rutgers University, Piscataway, New Jersey 08855-0939, USA.



Macromolecules
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 1
MoleculeChainsLengthOrganism
DNA (5'-D(*CP*GP*TP*(1AP)P*CP*(PT(NH3)3)G)-3')A6N/A
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PTN
Query on PTN

Download CCD File 
A
PLATINUM TRIAMINE ION
H9 N3 Pt
OMAFVUDQJABSNM-PHIGXVQTAM
 Ligand Interaction
SPM
Query on SPM

Download CCD File 
A
SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 25.193α = 90
b = 25.193β = 90
c = 38.948γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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