6RSO | pdb_00006rso

Structure of [Ru(phen)2(10-NO2-dppz)]2+ bound to the DNA sequence d(TCGGCGCCGA)

• PDB DOI: https://doi.org/10.2210/pdb6RSO/pdb
• NAKB: 6RSO

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


• Deposited: 2019-05-21 Released: 2020-07-08 
• Deposition Author(s): McQuaid, K.T., 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: 1.97 Å
• R-Value Free: 
  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Literature

Structure of [Ru(phen)2(10-NO2-dppz)]2+ bound to the DNA sequence d(TCGGCGCCGA)

McQuaid, K.T., Hall, J.P., Cardin, C.J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.95 kDa 
• Atom Count: 544 
• Modeled Residue Count: 20 
• Deposited Residue Count: 20 
• 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, B	10	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
KHN (Subject of Investigation/LOI)	D [auth A], F [auth B]	Ruthenium (bis-(phenanthroline)) (10-nitro-dipyridophenazine) C42 H26 N9 O2 Ru RRLMHIVRUDSXHL-UHFFFAOYSA-N
BA	C [auth A], E [auth B]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free:  0.247 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 4₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.73	α = 90
b = 46.73	β = 90
c = 31.99	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
xia2	data reduction
xia2	data scaling
PHASER	phasing
XDS	data reduction
XSCALE	data scaling
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-07-08 
Deposition Author(s): McQuaid, K.T., 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
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M004635/1

Revision History  

• Version 1.0: 2020-07-08
  Type: Initial release
  
• Version 1.1: 2021-02-10
  Changes: Derived calculations, Structure summary
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references, Refinement description