4MJ9 | pdb_00004mj9

lambda-[Ru(TAP)2(dppz-10-Me)]2+ bound to a synthetic DNA oligomer

• PDB DOI: https://doi.org/10.2210/pdb4MJ9/pdb
• NAKB: 4MJ9

• Classification: DNA
• Mutation(s): No 


• Deposited: 2013-09-03 Released: 2014-09-24 
• Deposition Author(s): Hall, J.P., Cardin, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free: 
  0.096 (Depositor), 0.100 (DCC) 
• R-Value Work: 
  0.086 (Depositor), 0.090 (DCC) 
• R-Value Observed: 
  0.086 (Depositor) 

Literature

The Structural Effect of Methyl Substitution on the Binding of Polypyridyl Ru dppz Complexes to DNA

Hall, J.P., Beer, H., Buchner, K., Cardin, D.J., Cardin, C.J.

(2015) Organometallics 

• DOI: https://doi.org/10.1021/om501208x

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 3.98 kDa 
• Atom Count: 372 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3')	A	10	N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2J0	B [auth A]	(10-methyldipyrido[3,2-a:2',3'-c]phenazine-kappa~2~N~4~,N~5~)[bis(pyrazino[2,3-f]quinoxaline-kappa~2~N~1~,N~10~)]ruthenium(2+) C39 H24 N12 Ru SUPGJTRQQWHNCH-UHFFFAOYSA-N
BA	C [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 0.97 Å
• R-Value Free:  0.096 (Depositor), 0.100 (DCC) 
• R-Value Work:  0.086 (Depositor), 0.090 (DCC) 
• R-Value Observed: 0.086 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.27	α = 90
b = 42.27	β = 90
c = 39.67	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
XDS	data reduction
Aimless	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Hall, J.P., Cardin, C.J.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2015-02-18
  Changes: Database references
• Version 1.2: 2015-05-13
  Changes: Database references
• Version 1.3: 2017-11-15
  Changes: Refinement description
• Version 1.4: 2024-02-28
  Changes: Data collection, Database references, Derived calculations