191D

CRYSTAL STRUCTURE OF INTERCALATED FOUR-STRANDED D(C3T)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.40 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.177 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of intercalated four-stranded d(C3T) at 1.4 angstroms resolution.

Kang, C.H.Berger, I.Lockshin, C.Ratliff, R.Moyzis, R.Rich, A.

(1994) Proc Natl Acad Sci U S A 91: 11636-11640

  • DOI: 10.1073/pnas.91.24.11636
  • Primary Citation of Related Structures:  
    191D

  • PubMed Abstract: 
  • The crystal structure of d(C3T), solved at 1.4 A resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. T ...

    The crystal structure of d(C3T), solved at 1.4 A resolution, reveals that the molecule forms a four-stranded intercalated complex. It consists of two parallel-stranded duplexes, each of which is held together by cytosine-protonated cytosine base pairs. The two duplexes are intercalated with each other and have opposite strand orientation. The molecule has a flat, lath-like appearance, and the covalently bonded cytosines have a slow right-handed twist of 17.1 degrees. However, there is considerable asymmetry. On one of the flat sides, the phosphate groups are rotated away from the center of the molecule. They are held in this orientation by bridging water molecules that bind the NH of cytosine and a phosphate group of an opposite chain. There is also considerable microheterogeneity in the structure. The cytosine hemiprotonation occurs even at pH 7 where stable crystals form.


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.



Macromolecules
  • Find similar nucleic acids by:  Sequence   |   Structure
  • Entity ID: 1
    MoleculeChainsLengthOrganismImage
    DNA (5'-D(*CP*CP*CP*T)-3')A, B, C, D4N/A
    Small Molecules
    Ligands 1 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    NA
    Query on NA

    Download Ideal Coordinates CCD File 
    A, B, C
    SODIUM ION
    Na
    FKNQFGJONOIPTF-UHFFFAOYSA-N
     Ligand Interaction
    Experimental Data & Validation

    Experimental Data

    • Method: X-RAY DIFFRACTION
    • Resolution: 1.40 Å
    • R-Value Free: 0.225 
    • R-Value Work: 0.177 
    • R-Value Observed: 0.177 
    • Space Group: C 2 2 21
    Unit Cell:
    Length ( Å )Angle ( ˚ )
    a = 28.281α = 90
    b = 44.341β = 90
    c = 50.472γ = 90
    Software Package:
    Software NamePurpose
    X-PLORrefinement

    Structure Validation

    View Full Validation Report



    Entry History 

    Deposition Data

    Revision History 

    • Version 1.0: 1994-11-30
      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: 2012-10-03
      Changes: Other