1JO2

Crystal Structure of the B-DNA Hexamer (CgATCG).Daunomycin Complex Containing a Ribose at the Intercalation Site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 

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This is version 1.3 of the entry. See complete history

Literature

Structure of a B-form DNA/RNA chimera (dC)(rG)d(ATCG) complexed with daunomycin at 1.5 A resolution.

Shi, K.Pan, B.Sundaralingam, M.

(2003) Acta Crystallogr.,Sect.D 59: 1377-1383


  • PubMed Abstract: 
  • The crystal structure of a DNA/RNA chimera (dC)(rG)d(ATCG) complexed with the anticancer drug daunomycin has been determined at 1.5 A resolution with R(work) and R(free) of 19.7 and 23.3%, respectively, for 2767 reflections. The complex crystallizes ...

    The crystal structure of a DNA/RNA chimera (dC)(rG)d(ATCG) complexed with the anticancer drug daunomycin has been determined at 1.5 A resolution with R(work) and R(free) of 19.7 and 23.3%, respectively, for 2767 reflections. The complex crystallizes in space group P4(1)2(1)2, with unit-cell parameters a = b = 28.05, c = 53.16 A, and contains one nucleic acid strand and one daunomycin molecule in the asymmetric unit. To our knowledge, this is the first crystal structure of a DNA/RNA chimera complexed with an intercalating drug. The DNA/RNA chimera adopts the B-form helical conformation, with the 2'-hydroxyl group in the major groove of the duplex, forming hydrogen bonds to N7 and the anionic phosphate oxygen of its 3'-side adenine. The present results indicate that the replacement by the ribose sugar in the DNA sequence does not change the geometry and intercalation pattern of daunomycin. A model of B-form RNA has been built based on the present structure. The model indicates that the interactions of the 2'-hydroxyl groups in the B-form duplex depend on their 3'-side nucleotides.


    Organizational Affiliation

    Departments of Chemistry and Biochemistry, The Ohio State University, 200 Johnston Laboratory, 176 West 19th Avenue, Columbus, OH 43210, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsLengthOrganism
5'-D(*C)-R(P*G)-D(P*AP*TP*CP*G)-3'A6N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DM1
Query on DM1

Download SDF File 
Download CCD File 
A
DAUNOMYCIN
DAUNORUBICIN
C27 H29 N O10
STQGQHZAVUOBTE-VGBVRHCVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.198 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 28.050α = 90.00
b = 28.050β = 90.00
c = 53.160γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-07-29
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-04
    Type: Refinement description