4LY2 | pdb_00004ly2

X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)

• PDB DOI: https://doi.org/10.2210/pdb4LY2/pdb
• NAKB: 4LY2

• Classification: DNA
• Mutation(s): No 


• Deposited: 2013-07-30 Released: 2014-09-24 
• Deposition Author(s): Niyazi, H., Teixeira, S., Mitchell, E., Forsyth, T., Cardin, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Literature

X-ray crystal structure of the ruthenium complex [Ru(phen)2(dppz)]2+ bound to d(TCGGTACCGA)

Niyazi, H., Teixeira, S., Mitchell, E., Forsyth, T., Cardin, C.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 4.67 kDa 
• Atom Count: 325 
• Modeled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA	A	10	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKP	B [auth A], C [auth A]	Lambda-Ru(phen)2(dppz) complex C42 H26 N8 Ru OYSRBLHMGIHFCB-UHFFFAOYSA-N
BA	D [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.219 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.45	α = 90
b = 52.45	β = 90
c = 32.58	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SHELXS	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-09-24 
Deposition Author(s): Niyazi, H., Teixeira, S., Mitchell, E., Forsyth, T., Cardin, C.

Revision History  

• Version 1.0: 2014-09-24
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Database references, Structure summary
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations