1D45

DNA DODECAMER C-G-C-G-A-A-T-T-C-G-C-G/HOECHST 33258 COMPLEX:-25 DEGREES C, PIPERAZINE DOWN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Observed: 0.152 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Low-temperature crystallographic analyses of the binding of Hoechst 33258 to the double-helical DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G.

Quintana, J.R.Lipanov, A.A.Dickerson, R.E.

(1991) Biochemistry 30: 10294-10306

  • DOI: 10.1021/bi00106a030
  • Primary Citation of Related Structures:  
    1D46, 1D45, 1D44, 1D43

  • PubMed Abstract: 
  • The crystal structure of the complex of Hoechst 33258 and the DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G has been solved from X-ray data collected at three different low temperatures (0, -25, and -100 degrees C). Such temperatures have permitted collection of higher resolution data (2 ...

    The crystal structure of the complex of Hoechst 33258 and the DNA dodecamer C-G-C-G-A-A-T-T-C-G-C-G has been solved from X-ray data collected at three different low temperatures (0, -25, and -100 degrees C). Such temperatures have permitted collection of higher resolution data (2.0, 1.9, and 2.0 A, respectively) than with previous X-ray studies of the same complex. In all three cases, the drug is located in the narrow central A-A-T-T region of the minor groove. Data analyses at -25 and -100 degrees C (each with a 1:1 drug/DNA ratio in the crystallizing solution) suggest a unique orientation for the drug. In contrast, two orientations of the drug were found equally possible at 0 degrees C with a 2:1 drug/DNA ratio in solution. Dihedral angles between the rings of Hoechst 33258 appear to change in a temperature-dependent manner. The drug/DNA complex is stabilized by single or bifurcated hydrogen bonds between the two N-H hydrogen-bond donors in the benzimidazole rings of Hoechst and adenine N3 and thymine O2 acceptors in the minor groove. A general preference for AT regions is conferred by electrostatic potential and by narrowing of the walls of the groove. Local point-by-point AT specificity follows from close van der Waals contacts between ring hydrogen atoms in Hoechst 33258 and the C2 hydrogens of adenines. Replacement of one benzimidazole ring by purine in a longer chain analogue of Hoechst 33258 could make that particular site GC tolerant in the manner observed at imidazole substitution for pyrrole in lexitropsins.


    Related Citations: 
    • The Molecular Structure of the Complex of Hoechst 33258 and the DNA Dodecamer d(CGCGAATTCGCG)
      Teng, M., Usman, N., Frederick, C.A., Wang, A.H.-J.
      (1988) Nucleic Acids Res 16: 2671
    • Binding of Hoechst 33258 to the Minor Groove of B-DNA
      Pjura, P.E., Grzeskowiak, K., Dickerson, R.E.
      (1987) J Mol Biol 196: 257
    • Isohelical Analysis of DNA Groove-Binding Drugs
      Goodsell, D., Dickerson, R.E.
      (1986) J Med Chem 29: 727

    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of California, Los Angeles 90024-1570.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')A, B12N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    HT
    Query on HT

    Download Ideal Coordinates CCD File 
    C [auth A]2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE
    C25 H24 N6 O
    INAAIJLSXJJHOZ-UHFFFAOYSA-N
     Ligand Interaction
    MG
    Query on MG

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

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.90 Å
    • R-Value Observed: 0.152 
    • Space Group: P 21 21 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 23.89α = 90
    b = 38.52β = 90
    c = 66.34γ = 90
    Software Package:
    Software NamePurpose
    NUCLSQrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 1992-04-15
      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: 2011-08-24
      Changes: Atomic model