4JD8

Racemic-[Ru(phen)2(dppz)]2+] bound to synthetic DNA at high resolution

• PDB DOI: https://doi.org/10.2210/pdb4JD8/pdb
• Entry: 4JD8 supersedes: 4E87
• NAKB: 4JD8

• Classification: DNA
• Mutation(s): No 


• Deposited: 2013-02-24 Released: 2013-04-24 
• Deposition Author(s): Cook, D.S., Hall, J.P., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free: 
  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work: 
  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 
  0.139 (Depositor) 

Starting Model: experimental

Literature

X-ray Crystal Structure of rac-[Ru(phen)2dppz](2+) with d(ATGCAT)2 Shows Enantiomer Orientations and Water Ordering.

Hall, J.P., Cook, D., Morte, S.R., McIntyre, P., Buchner, K., Beer, H., Cardin, D.J., Brazier, J.A., Winter, G., Kelly, J.M., Cardin, C.J.

(2013) J Am Chem Soc 135: 12652-12659

• PubMed: 23875832 
• DOI: https://doi.org/10.1021/ja403590e
• Primary Citation of Related Structures:  
  4JD8


• PubMed Abstract: 
  

  We report an atomic resolution X-ray crystal structure containing both enantiomers of rac-[Ru(phen)2dppz](2+) with the d(ATGCAT)2 DNA duplex (phen = phenanthroline; dppz = dipyridophenazine). The first example of any enantiomeric pair crystallized with a DNA duplex shows different orientations of the Λ and Δ binding sites, separated by a clearly defined structured water monolayer. Job plots show that the same species is present in solution. Each enantiomer is bound at a TG/CA step and shows intercalation from the minor groove. One water molecule is directly located on one phenazine N atom in the Δ-enantiomer only.

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Organizational Affiliation: 

Chemistry Department, University of Reading, Whiteknights, Reading RG6 AD, United Kingdom.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 5.14 kDa 
• Atom Count: 438 
• Modelled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*TP*GP*CP*AP*T)-3')	A, B	6	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKP	D [auth B]	Lambda-Ru(phen)2(dppz) complex C42 H26 N8 Ru OYSRBLHMGIHFCB-UHFFFAOYSA-N
0TN	C [auth B]	Delta-Ru(phen)2(dppz) complex C42 H26 N8 Ru OYSRBLHMGIHFCB-UHFFFAOYSA-N
K	E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.16 Å
• R-Value Free:  0.162 (Depositor), 0.160 (DCC) 
• R-Value Work:  0.138 (Depositor), 0.140 (DCC) 
• R-Value Observed: 0.139 (Depositor) 

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.55	α = 90
b = 37.55	β = 90
c = 54.371	γ = 120

Software Package:

Software Name	Purpose
GDA	data collection
PHASER	phasing
PHENIX	refinement
MOSFLM	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Cook, D.S., Hall, J.P., Cardin, C.J.
• This entry supersedes: 4E87

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2013-09-18
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description