238D | pdb_0000238d

CRYSTAL STRUCTURE OF THE DNA DECAMER D(AGG(BR)CATGCCT): COMPARISON WITH D(AGGCATGCCT) AND IMPLICATIONS FOR COBALT HEXAMMINE BINDING TO DNA

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 1995-11-02 Released: 1996-01-30 
  • Deposition Author(s): Nunn, C.M.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work: 
    0.196 (Depositor) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history. 

Literature

Crystal structure of d(AGGBrCATGCCT): implications for cobalt hexammine binding to DNA

Nunn, C.M.

(1996) J Biomol Struct Dyn 14: 49-56

  • DOI: https://doi.org/10.1080/07391102.1996.10508928
  • Primary Citation Related Structures: 
    238D

  • PubMed Abstract: 

    The crystal structure of the DNA decamer d(AGGBrCATGCCT) has been determined to a resolution of 2.0 A and R factor of 19.6%. Crystals of d(AGGBrCATGCCT) were grown in the presence of cobalt hexammine but no cobalt hexammine ions are bound to the DNA structure. This contrasts with the recently determined crystal structure of d(AGGCATGCCT) which has a similar DNA conformation and cobalt hexammine ions bound directly to the DNA. Comparison with the structure of d(AGGCATGCCT) and appreciation of the crystal packing of this sequence leads to an understanding of how cobalt hexammine binding to DNA occurs and its role in determining DNA conformation.

    • Organizational Affiliation: 
    • CRC Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K. c.nunn@icr.ac.uk

Macromolecule Content 

  • Total Structure Weight: 3.12 kDa 
  • Atom Count: 259 
  • Modeled Residue Count: 10 
  • Deposited Residue Count: 10 
  • Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*AP*GP*GP*(CBR)P*AP*TP*GP*CP*CP*T)-3')10N/A
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Work:  0.196 (Depositor) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.2α = 90
b = 33.2β = 90
c = 77.1γ = 120
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 1996-01-30 
    • Deposition Author(s): Nunn, C.M.

Revision History  (Full details and data files)

  • Version 1.0: 1996-01-30
    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: 2024-02-14
    Changes: Data collection, Database references, Derived calculations