3LPV

X-ray crystal structure of duplex DNA containing a cisplatin 1,2-d(GpG) intrastrand cross-link

  • Classification: DNA
  • Mutation(s): No 

  • Deposited: 2010-02-06 Released: 2010-08-11 
  • Deposition Author(s): Todd, R.C., Lippard, S.J.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.77 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.172 
  • R-Value Observed: 0.173 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of duplex DNA containing the cisplatin 1,2-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link at 1.77A resolution.

Todd, R.C.Lippard, S.J.

(2010) J Inorg Biochem 104: 902-908

  • DOI: 10.1016/j.jinorgbio.2010.04.005
  • Primary Citation of Related Structures:  
    3LPV

  • PubMed Abstract: 
  • We report the 1.77-A resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5'-CCTCTGGTCTCC-3' that has been modified to contain a single engineered 1,2-cis-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2 ...

    We report the 1.77-A resolution X-ray crystal structure of a dodecamer DNA duplex with the sequence 5'-CCTCTGGTCTCC-3' that has been modified to contain a single engineered 1,2-cis-{Pt(NH(3))(2)}(2+)-d(GpG) cross-link, the major DNA adduct of cisplatin. These data represent a significant improvement in resolution over the previously published 2.6-A structure. The ammine ligands in this structure are clearly resolved, leading to improved visualization of the cross-link geometry with respect to both the platinum center and to the nucleobases, which adopt a higher energy conformation. Also better resolved are the deoxyribose sugar puckers, which allow us to re-examine the global structure of platinum-modified DNA. Another new feature of this model is the location of four octahedral [Mg(H(2)O)(6)](2+) ions associated with bases in the DNA major groove and the identification of 124 ordered water molecules that participate in hydrogen-bonding interactions with either the nucleic acid or the diammineplatinum(II) moiety.


    Organizational Affiliation

    Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, United States.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*CP*TP*CP*TP*GP*GP*TP*CP*TP*CP*C)-3'A, C12N/A
    Protein Feature View
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    • Reference Sequence
    • Find similar nucleic acids by:  Sequence   |   Structure
    • Entity ID: 2
      MoleculeChainsLengthOrganismImage
      5'-D(*GP*GP*AP*GP*AP*CP*CP*AP*GP*AP*GP*G)-3'B, D12N/A
      Protein Feature View
      Expand
      • Reference Sequence
      Experimental Data & Validation

      Experimental Data

      • Method: X-RAY DIFFRACTION
      • Resolution: 1.77 Å
      • R-Value Free: 0.198 
      • R-Value Work: 0.172 
      • R-Value Observed: 0.173 
      • Space Group: P 1
      Unit Cell:
      Length ( Å )Angle ( ˚ )
      a = 31.303α = 80.06
      b = 35.425β = 84.09
      c = 45.128γ = 81.77
      Software Package:
      Software NamePurpose
      DENZOdata reduction
      SCALEPACKdata scaling
      PHASERphasing
      REFMACrefinement
      PDB_EXTRACTdata extraction
      HKL-2000data collection
      HKL-2000data reduction
      HKL-2000data scaling

      Structure Validation

      View Full Validation Report




      Entry History 

      Deposition Data

      Revision History  (Full details and data files)

      • Version 1.0: 2010-08-11
        Type: Initial release
      • Version 1.1: 2011-07-13
        Changes: Version format compliance
      • Version 1.2: 2017-11-01
        Changes: Refinement description