1EM0

COMPLEX OF D(CCTAGG) WITH TETRA-[N-METHYL-PYRIDYL] PORPHYRIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.90 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.152 
  • R-Value Observed: 0.152 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A DNA-porphyrin minor-groove complex at atomic resolution: the structural consequences of porphyrin ruffling.

Bennett, M.Krah, A.Wien, F.Garman, E.McKenna, R.Sanderson, M.Neidle, S.

(2000) Proc Natl Acad Sci U S A 97: 9476-9481

  • DOI: 10.1073/pnas.160271897
  • Primary Citation of Related Structures:  
    1EM0

  • PubMed Abstract: 
  • The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0 ...

    The crystal structure of a B-type DNA hexanucleotide duplex complexed with the porphyrin molecule nickel-[tetra-N-methyl-pyridyl] porphyrin has been solved by multiwavelength anomalous diffraction phasing and refined to an R factor of 11.5% at a resolution of 0.9 A. The structure has been solved and refined as two crystallographically independent duplexes, stacked end to end. Contrary to expectation, the porphyrin molecule is not intercalated into the duplex but is stacked onto the ends of the two-duplex stack. The porphyrin molecule is highly buckled as a consequence of the nickel coordination, which produces large changes in local DNA structure. A second mode of porphyrin binding is apparent as a consequence of crystal packing, which places the ligand in the minor groove of an adjacent duplex. This structure thus provides, to our knowledge, the first atomic visualization of minor-groove binding for a porphyrin molecule. The geometry of groove binding provides a ready explanation for porphyrin-induced DNA strand cleavage at deoxyribose residues.


    Organizational Affiliation

    The Randall Institute, Department of Biomedical Sciences, King's College London, United Kingdom.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*(CBR)P*CP*TP*AP*GP*G)-3')A, B, C, D6N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    PNI (Subject of Investigation/LOI)
    Query on PNI

    Download Ideal Coordinates CCD File 
    F [auth B], H [auth D]TETRA[N-METHYL-PYRIDYL] PORPHYRIN-NICKEL
    C44 H36 N8 Ni
    KZZFAYDWICISAM-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

    Download Ideal Coordinates CCD File 
    E [auth A], G [auth C]MAGNESIUM ION
    Mg
    JLVVSXFLKOJNIY-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 0.90 Å
    • R-Value Free: 0.172 
    • R-Value Work: 0.152 
    • R-Value Observed: 0.152 
    • Space Group: P 41
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 32.21α = 90
    b = 32.21β = 90
    c = 62.257γ = 90
    Software Package:
    Software NamePurpose
    CCP4model building
    SHELXL-97refinement
    DENZOdata reduction
    SCALEPACKdata scaling
    CCP4phasing

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2000-08-21
      Type: Initial release
    • Version 1.1: 2008-04-27
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance