1D32 | pdb_00001d32

DRUG-INDUCED DNA REPAIR: X-RAY STRUCTURE OF A DNA-DITERCALINIUM COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb1D32/pdb
• NAKB: 1D32

• Classification: DNA
• Mutation(s): No 


• Deposited: 1991-01-23 Released: 1992-04-15 
• Deposition Author(s): Gao, Q., Williams, L.D., Egli, M., Rabinovich, D., Chen, S.-L., Quigley, G.J., Rich, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 
  0.225 (Depositor) 

Literature

Drug-induced DNA repair: X-ray structure of a DNA-ditercalinium complex.

Gao, Q., Williams, L.D., Egli, M., Rabinovich, D., Chen, S.L., Quigley, G.J., Rich, A.

(1991) Proc Natl Acad Sci U S A 88: 2422-2426

• PubMed: 2006181 
• DOI: https://doi.org/10.1073/pnas.88.6.2422
• Primary Citation Related Structures: 
  1D32


• PubMed Abstract: 
  

  Ditercalinium is a synthetic anticancer drug that binds to DNA by bis-intercalation and activates DNA repair processes. In prokaryotes, noncovalent DNA-ditercalinium complexes are incorrectly recognized by the uvrABC repair system as covalent lesions on DNA. In eukaryotes, mitochondrial DNA is degraded by excess and futile DNA repair. Using x-ray crystallography, we have determined, to 1.7 A resolution, the three-dimensional structure of a complex of ditercalinium bound to the double-stranded DNA fragment [d(CGCG)]2. The DNA in the complex with ditercalinium is kinked (by 15 degrees) and severely unwound (by 36 degrees) with exceptionally wide major and minor grooves. Recognition of the DNA-ditercalinium complex by uvrABC in prokaryotes, and by mitochondrial DNA repair systems in eukaryotes, might be related to drug-induced distortion of the DNA helix.

---

Organizational Affiliation: 
• Department of Biology, Massachusetts Institute of Technology, Cambridge 02139.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.1 kDa 
• Atom Count: 295 
• Modeled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*G)-3')	A, B	4	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DIT	C [auth A]	DITERCALINIUM C46 H50 N6 O2 NHUWXMNVGMRODJ-UHFFFAOYSA-P

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 26.88	α = 90
b = 26.88	β = 90
c = 82.6	γ = 90

Software Package:

Software Name	Purpose
NUCLSQ	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 1992-04-15 
Deposition Author(s): Gao, Q., Williams, L.D., Egli, M., Rabinovich, D., Chen, S.-L., Quigley, G.J., Rich, A.

Revision History  

• 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: 2024-02-07
  Changes: Data collection, Database references, Derived calculations