6F3C | pdb_00006f3c

The cytotoxic [Pt(H2bapbpy)] platinum complex interacting with the CGTACG hexamer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 
    0.292 (Depositor), 0.285 (DCC) 
  • R-Value Work: 
    0.257 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 
    0.261 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Induction of a Four-Way Junction Structure in the DNA Palindromic Hexanucleotide 5'-d(CGTACG)-3' by a Mononuclear Platinum Complex.

van Rixel, V.H.S.Busemann, A.Wissingh, M.F.Hopkins, S.L.Siewert, B.van de Griend, C.Siegler, M.A.Marzo, T.Papi, F.Ferraroni, M.Gratteri, P.Bazzicalupi, C.Messori, L.Bonnet, S.

(2019) Angew Chem Int Ed Engl 58: 9378-9382

  • DOI: https://doi.org/10.1002/anie.201814532
  • Primary Citation Related Structures: 
    6F3C

  • PubMed Abstract: 

    Four-way junctions (4WJs) are supramolecular DNA assemblies comprising four interacting DNA strands that in biology are involved in DNA-damage repair. In this study, a new mononuclear platinum(II) complex 1 was prepared that is capable of driving the crystallization of the DNA oligomer 5'-d(CGTACG)-3' specifically into a 4WJ-like motif. In the crystal structure of the 1-CGTACG adduct, the distorted-square-planar platinum complex binds to the core of the 4WJ-like motif through π-π stacking and hydrogen bonding, without forming any platinum-nitrogen coordination bonds. Our observations suggest that the specific molecular properties of the metal complex are crucially responsible for triggering the selective assembly of this peculiar DNA superstructure.


  • Organizational Affiliation
    • Leiden Institute of Chemistry, Leiden University, Einsteinweg 55, PO Box 9502, 2333CC, Leiden, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 7.75 kDa 
  • Atom Count: 506 
  • Modeled Residue Count: 22 
  • Deposited Residue Count: 22 
  • Unique nucleic acid chains: 2

Macromolecules

Find similar nucleic acids by:  Sequence
Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*AP*CP*G)-3')A [auth B],
B [auth D]
6synthetic construct
Sequence Annotations
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Reference Sequence
Find similar nucleic acids by:  Sequence
Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*TP*AP*CP*G)-3')C,
D [auth A]
5synthetic construct
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free:  0.292 (Depositor), 0.285 (DCC) 
  • R-Value Work:  0.257 (Depositor), 0.273 (DCC) 
  • R-Value Observed: 0.261 (Depositor) 
Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 30.09α = 90
b = 30.09β = 90
c = 116.99γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-29
    Type: Initial release
  • Version 1.1: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-07
    Changes: Data collection, Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description