1JUX

1.6A Resolution Crystal Structures of the DNA Octamers d(IUATATAC) and d(ITITACAC):Binding of Two Distamycin Drugs Side-by-Side

• PDB DOI: https://doi.org/10.2210/pdb1JUX/pdb
• NAKB: 1JUX

• Classification: DNA
• Mutation(s): No 


• Deposited: 2001-08-28 Released: 2004-01-27 
• Deposition Author(s): Deng, J., Pan, B., Sundaralingam, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 

Literature

Structure of d(ITITACAC) complexed with distamycin at 1.6 A resolution.

Deng, J., Pan, B., Sundaralingam, M.

(2003) Acta Crystallogr D Biol Crystallogr 59: 2342-2344

• PubMed: 14646114 
• DOI: https://doi.org/10.1107/s0907444903020730
• Primary Citation of Related Structures:  
  1JUX


• PubMed Abstract: 
  

  The crystal structure of the DNA octamer d(ITITACAC)(2) complexed with distamycin has been determined at 1.6 A resolution and refined to a final R(work) and R(free) of 17.0 and 20.7%, respectively. Two molecules of distamycin bind to the DNA duplex in an antiparallel side-by-side fashion. Each drug molecule covers five base pairs of the DNA duplex, with its amide groups hydrogen-bonding to bases in the proximal DNA strand. These two antiparallel drug molecules are stacked together with the pyrrole rings of one molecule stacking against the amide groups of the other. The present structure emphasizes the features of alternating DNA octamers in interaction with distamycin.

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Organizational Affiliation: 

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

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 2.88 kDa 
• Atom Count: 230 
• Modelled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*IP*TP*IP*TP*AP*CP*AP*C)-3'	A	8	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DMY	B [auth A]	DISTAMYCIN A C22 H27 N9 O4 UPBAOYRENQEPJO-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.179 
• R-Value Work: 0.149 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.26	α = 90
b = 25.05	β = 124.23
c = 28.3	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-01-27 
Deposition Author(s): Deng, J., Pan, B., Sundaralingam, M.

Revision History  

• Version 1.0: 2004-01-27
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-04
  Changes: Refinement description
• Version 1.4: 2024-02-07
  Changes: Data collection, Database references, Derived calculations