263D | pdb_0000263d

ISOHELICITY AND PHASING IN DRUG-DNA SEQUENCE RECOGNITION: CRYSTAL STRUCTURE OF A TRIS(BENZIMIDAZOLE)-OLIGONUCLEOTIDE COMPLEX

• PDB DOI: https://doi.org/10.2210/pdb263D/pdb
• NAKB: 263D

• Classification: DNA
• Mutation(s): No 


• Deposited: 1996-09-27 Released: 1996-10-15 
• Deposition Author(s): Clark, G.R., Gray, E.J., Neidle, S., Li, Y.-H., Leupin, W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work: 
  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Isohelicity and phasing in drug--DNA sequence recognition: crystal structure of a tris(benzimidazole)--oligonucleotide complex.

Clark, G.R., Gray, E.J., Neidle, S., Li, Y.H., Leupin, W.

(1996) Biochemistry 35: 13745-13752

• PubMed: 8901516 
• DOI: https://doi.org/10.1021/bi960421m
• Primary Citation Related Structures: 
  263D


• PubMed Abstract: 
  

  The crystal structure is reported of a tris(benzimidazole) analogue of the minor-groove drug Hoechst 33258 bound to the sequence d(CGCAAATTTGCG)2. The structure has been refined to an R factor of 17.4% at a resolution of 2.2 A. The ligand covers approximately 7 1/2 base pairs, including the 5'-AAATTT central sequence. This has an exceptionally narrow minor-groove width, together with high propeller twists for individual base pairs. The ligand has a highly twisted structure, with an overall twist of 50 degrees between aromatic rings. All three benzimidazole subunits are in register with the DNA, and there is a symmetric group of six hydrogen bonds between ligand and A.T base-pair edges. By contrast, the ligand does not show an optimal isohelical fit to the DNA. The correct phasing of drug and DNA base pairs is ensured by a number of changes to the DNA such that the central 5'-AAATTT region is slightly unwound relative to the structures of other noncovalent minor-groove drug complexes.

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Organizational Affiliation: 
• CRC Biomolecular Structure Unit, Institute of Cancer Research, Sutton, Surrey, U.K.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 7.87 kDa 
• Atom Count: 588 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3')	A, B	12	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TBZ	C [auth B]	2''-(4-METHOXYPHENYL)-5-(3-AMINO-1-PYRROLIDINYL)-2,5',2',5''-TRI-BENZIMIDAZOLE C32 H29 N8 O MEDNUDGNJOXVKL-NRFANRHFSA-O

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Work:  0.174 (Depositor), 0.186 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.7	α = 90
b = 40.82	β = 90
c = 64.9	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
XENGEN	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 1996-10-15 
Deposition Author(s): Clark, G.R., Gray, E.J., Neidle, S., Li, Y.-H., Leupin, W.

Revision History  

• Version 1.0: 1996-10-15
  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: 2024-02-14
  Changes: Data collection, Database references, Derived calculations
• Version 1.4: 2024-04-03
  Changes: Refinement description