3GSK

A Bulky Rhodium Complex Bound to an Adenosine-Adenosine DNA Mismatch


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode

Zeglis, B.M.Pierre, V.C.Kaiser, J.T.Barton, J.K.

(2009) Biochemistry 48: 4247-4253

  • DOI: 10.1021/bi900194e
  • Primary Citation of Related Structures:  
    3GSJ, 3GSK

  • PubMed Abstract: 
  • Two crystal structures of Delta-Rh(bpy)(2)(chrysi)(3+) (chrysi is 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5'-CGGAAATTACCG-3' containing two adenosine-adenosine mismatches (italics) through metalloinsertion were determined. Diffraction quality crystals with two different space groups (P3(2)21 and P4(3)2(1)2) were obtained under very similar crystallization conditions ...

    Two crystal structures of Delta-Rh(bpy)(2)(chrysi)(3+) (chrysi is 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5'-CGGAAATTACCG-3' containing two adenosine-adenosine mismatches (italics) through metalloinsertion were determined. Diffraction quality crystals with two different space groups (P3(2)21 and P4(3)2(1)2) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2'-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5'-AT-3' step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Delta-Rh(bpy)(2)(chrysi)(3+) bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single-base mismatches. These results underscore the generality of metalloinsertion as a new mode of noncovalent binding by small molecules with a DNA duplex.


    Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    5'-D(*CP*GP*GP*AP*AP*AP*TP*TP*AP*CP*CP*G)-3'B [auth A], A [auth B]12N/A
    Protein Feature View
    Expand
    • Reference Sequence
    Small Molecules
    Ligands 2 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    R1C
    Query on R1C

    Download Ideal Coordinates CCD File 
    C [auth B], E [auth A]bis(2,2'-bipyridine-kappa~2~N~1~,N~1'~)[chrysene-5,6-diiminato(2-)-kappa~2~N,N']rhodium(4+)
    C38 H26 N6 Rh
    UKDZOHAQCIISRY-UHFFFAOYSA-N
     Ligand Interaction
    CAC
    Query on CAC

    Download Ideal Coordinates CCD File 
    D [auth B]CACODYLATE ION
    C2 H6 As O2
    OGGXGZAMXPVRFZ-UHFFFAOYSA-M
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.60 Å
    • R-Value Free: 0.227 
    • R-Value Work: 0.184 
    • R-Value Observed: 0.186 
    • Space Group: P 32 2 1
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 48.337α = 90
    b = 48.337β = 90
    c = 69.505γ = 120
    Software Package:
    Software NamePurpose
    Blu-Icedata collection
    SHELXDphasing
    PHENIXrefinement
    MOSFLMdata reduction
    SCALAdata scaling

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History  (Full details and data files)

    • Version 1.0: 2009-05-19
      Type: Initial release
    • Version 1.1: 2011-07-13
      Changes: Non-polymer description, Version format compliance
    • Version 1.2: 2018-02-14
      Changes: Experimental preparation