159D

SIDE BY SIDE BINDING OF TWO DISTAMYCIN A DRUGS IN THE MINOR GROOVE OF AN ALTERNATING B-DNA DUPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Work: 0.150 
  • R-Value Observed: 0.150 

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This is version 1.2 of the entry. See complete history


Literature

Binding of two distamycin A molecules in the minor groove of an alternating B-DNA duplex.

Chen, X.Ramakrishnan, B.Rao, S.T.Sundaralingam, M.

(1994) Nat Struct Biol 1: 169-175

  • DOI: 10.1038/nsb0394-169
  • Primary Citation of Related Structures:  
    159D

  • PubMed Abstract: 
  • Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in the expanded minor groove ...

    Here we report the 1.8A X-ray structure of a 2:1 drug-DNA complex between distamycin A and an alternating B-DNA octamer duplex d(ICICICIC)2. The two distamycin A molecules are bound side by side with dyad symmetry in an antiparallel orientation in the expanded minor groove. The amides of each drug molecule are hydrogen bonded to the minor groove base atoms of only one DNA strand. The complex not only shows binding of two drug molecules, but the DNA duplex also exhibits striking low-high alternations in the helical twist angles, the sugar puckering and the phosphate conformations, providing the basis for a new model for an alternating B-DNA with a dinucleotide repeat.


    Organizational Affiliation

    Department of Chemistry, Ohio State University, Columbus 43210, USA.



Macromolecules
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  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*IP*CP*IP*CP*IP*CP*IP*C)-3')A8N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    DMY (Subject of Investigation/LOI)
    Query on DMY

    Download Ideal Coordinates CCD File 
    B [auth A]DISTAMYCIN A
    C22 H27 N9 O4
    UPBAOYRENQEPJO-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.80 Å
    • R-Value Work: 0.150 
    • R-Value Observed: 0.150 
    • Space Group: P 41 2 2
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 27.93α = 90
    b = 27.93β = 90
    c = 57.67γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement

    Structure Validation

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    Ligand Structure Quality Assessment  



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1995-02-07
      Type: Initial release
    • Version 1.1: 2008-05-22
      Changes: Version format compliance
    • Version 1.2: 2011-07-13
      Changes: Version format compliance