5BNA

THE PRIMARY MODE OF BINDING OF CISPLATIN TO A B-DNA DODECAMER: C-G-C-G-A-A-T-T-C-G-C-G


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.102 

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This is version 1.3 of the entry. See complete history


Literature

The primary mode of binding of cisplatin to a B-DNA dodecamer: C-G-C-G-A-A-T-T-C-G-C-G

Wing, R.M.Pjura, P.Drew, H.R.Dickerson, R.E.

(1984) EMBO J 3: 1201-1206

  • DOI: https://doi.org/10.1002/j.1460-2075.1984.tb01951.x
  • Primary Citation of Related Structures:  
    5BNA

  • PubMed Abstract: 

    When cisplatin [cis- diamminodichloroplatinum (II)] is diffused into pre-grown crystals of the B-DNA double-helical dodecamer C-G-C-G-A-A-T-T-C-G-C-G, it binds preferentially to the N7 positions of guanines, with what probably is an aquo bridge between Pt and the adjacent O6 atom of the same guanine. The entire guanine ring moves slightly toward the platinum site, into the major groove. Only three of the eight potential cisplatin binding sites on guanines actually are occupied, and this differential reactivity can be explained in terms of the relative freedom of motion of guanines toward the major groove. This shift of guanines upon ligation may weaken the glycosyl bond and assist in the depurination that leads to mismatch SOS repair and G.C. to T.A. transversion.


Macromolecules

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Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
A, B
12N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Observed: 0.102 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 24.16α = 90
b = 39.93β = 90
c = 66.12γ = 90
Software Package:
Software NamePurpose
JACK-LEVITTrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1983-11-02
    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: 2024-03-06
    Changes: Data collection, Database references, Derived calculations