4X18 | pdb_00004x18

[Ru(TAP)2(dppz-11-Me)]2+ bound to d(TCGGCGCCGA)

• PDB DOI: https://doi.org/10.2210/pdb4X18/pdb
• NAKB: 4X18

• Classification: DNA
• Organism(s): synthetic construct
• Mutation(s): No 


• Deposited: 2014-11-24 Released: 2015-05-13 
• Deposition Author(s): Hall, J.P., Cardin, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.05 Å
• R-Value Free: 
  0.105 (Depositor), 0.120 (DCC) 
• R-Value Work: 
  0.096 (Depositor), 0.100 (DCC) 
• R-Value Observed: 
  0.096 (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: 333 
• 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	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKM	B [auth A]	(11-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 C39 H24 N12 Ru IUORKEDPZTZOCS-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: 1.05 Å
• R-Value Free:  0.105 (Depositor), 0.120 (DCC) 
• R-Value Work:  0.096 (Depositor), 0.100 (DCC) 
• R-Value Observed: 0.096 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.16	α = 90
b = 42.16	β = 90
c = 39.17	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
SHELX	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Hall, J.P., Cardin, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/K019279/1

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Advisory, Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations