1ZPH

Crystal structure analysis of the minor groove binding quinolinium quaternary salt SN 8315 complexed with CGCGAATTCGCG

• PDB DOI: https://doi.org/10.2210/pdb1ZPH/pdb
• NAKB: 1ZPH

• Classification: DNA
• Mutation(s): No 


• Deposited: 2005-05-16 Released: 2005-10-11 
• Deposition Author(s): Adams, A., Leong, C., Denny, W.A., Guss, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.314 
• R-Value Work: 0.234 
• R-Value Observed: 0.240 

Literature

Structures of two minor-groove-binding quinolinium quaternary salts complexed with d(CGCGAATTCGCG)(2) at 1.6 and 1.8 Angstrom resolution.

Adams, A., Leong, C., Denny, W.A., Guss, J.M.

(2005) Acta Crystallogr D Biol Crystallogr 61: 1348-1353

• PubMed: 16204886 
• DOI: https://doi.org/10.1107/S0907444905022997
• Primary Citation of Related Structures:  
  1ZPH, 1ZPI


• PubMed Abstract: 
  

  The structures of the complexes formed between two anticancer minor-groove-binding quinolinium quaternary salts and the dodecamer d(CGCGAATTCGCG)(2) have been refined to resolutions of 1.6 and 1.8 Angstrom. The complexes crystallized in space group P2(1)2(1)2(1) and the structures are isomorphous with previously solved dodecamer structures. The ligands both bind in the central AT region of the minor groove and although the crystallization conditions and structures of the ligands are very similar, they bind in opposing orientations. The structures are compared with two previously published structures of quinolinium quaternary salts, refined at 2.5 Angstrom resolution, complexed with d(CGCGAATTCGCG)(2) and an e(6)G-modified DNA.

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Organizational Affiliation: 

School of Molecular and Microbial Biosciences, University of Sydney, NSW 2006, Australia. [e-mail]

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 7.84 kDa 
• Atom Count: 556 
• Modelled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SN8	D [auth B]	1,6-DIMETHYL-4-(4-(4-(1-METHYLPYRIDINIUM-4-YLAMINO)PHENYLCARBAMOYL)PHENYLAMINO)QUINOLINIUM C30 H47 N5 O VJDMGOLLSXKCPI-DHBIPOTOSA-N
MG	C [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.314 
• R-Value Work: 0.234 
• R-Value Observed: 0.240 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 24.873	α = 90
b = 39.907	β = 90
c = 65.707	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-10-11 
Deposition Author(s): Adams, A., Leong, C., Denny, W.A., Guss, J.M.

Revision History  

• Version 1.0: 2005-10-11
  Type: Initial release
  
• Version 1.1: 2008-04-30
  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