4YMC | pdb_00004ymc

Lambda-[Ru(TAP)2(dppz)]2+ bound to d(CCGGATCCGG)2

• PDB DOI: https://doi.org/10.2210/pdb4YMC/pdb
• NAKB: 4YMC

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


• Deposited: 2015-03-06 Released: 2016-03-23 
• Deposition Author(s): Gurung, S.P., 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: 1.88 Å
• R-Value Free: 
  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.198 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.200 (Depositor) 

Literature

Reversal of a single base pair step controls guanine photo-oxidation by an intercalating Ru(II) dipyridophenazine complex.

Keane, P.M., Gurung, S.P., Niyazi, H., Poynton, F.E., Hall, J.P., Sazanovich, I.V., Towrie, M., Teixeira, S., Mitchell, E., Forsyth, T., Gunnlaugsson, T., Quinn, S.J., Cardin, C.J., Kelly, J.M.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 3.97 kDa 
• Atom Count: 275 
• 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(*CP*CP*GP*GP*AP*TP*CP*CP*GP*G)-3')	A	10	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKL	C [auth A]	Ru(tap)2(dppz) complex C38 H22 N12 Ru PIKVAZQLFXBUSD-UHFFFAOYSA-N
BA	B [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: 1.88 Å
• R-Value Free:  0.257 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.198 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.200 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.38	α = 90
b = 47.38	β = 90
c = 33.83	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Coot	model building
SHELX	phasing
xia2	data scaling

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Gurung, S.P., 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: 2016-03-23
  Type: Initial release
  
• Version 2.0: 2017-08-30
  Changes: Atomic model, Author supporting evidence, Derived calculations
• Version 2.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations
• Version 3.0: 2026-08-26
  Type: Remediation
  Reason: Metalloprotein remediation
  Changes: Derived calculations, Non-polymer description, Structure summary