3UYB

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

• PDB DOI: https://doi.org/10.2210/pdb3UYB/pdb
• Entry: 3UYB supersedes: 3UYA
• NAKB: 3UYB

• Classification: DNA
• Mutation(s): No 


• Deposited: 2011-12-06 Released: 2013-01-16 
• Deposition Author(s): Niyazi, H.N., Texeira, S.C.M., Mitchell, E.P., Cardin, J.C., Forsyth, V.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.167 
• R-Value Work: 0.127 
• R-Value Observed: 0.129 

Literature

Crystal structure of lambda-[Ru(TAP)2(dppz)]2+ with d(TCGGTACCGA)2 displaying kinking of DNA via semiintercalation.

Niyazi, H.N., O'Sullivan, K., Texeira, S.C.M., Mitchell, E.P., Kelly, J.M., Cardin, J.C., Forsyth, V.T.

To be published.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 4.68 kDa 
• Atom Count: 376 
• Modelled Residue Count: 10 
• Deposited Residue Count: 10 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKL	B [auth A], C [auth A]	Ru(tap)2(dppz) complex C38 H22 N12 Ru PIKVAZQLFXBUSD-UHFFFAOYSA-N
BA	D [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.167 
• R-Value Work: 0.127 
• R-Value Observed: 0.129 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.376	α = 90
b = 54.376	β = 90
c = 28.995	γ = 90

Software Package:

Software Name	Purpose
MxCuBE	data collection
SHELXCD	phasing
SHELXE	model building
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-01-16 
Deposition Author(s): Niyazi, H.N., Texeira, S.C.M., Mitchell, E.P., Cardin, J.C., Forsyth, V.T.
• This entry supersedes: 3UYA

Revision History  

• Version 1.0: 2013-01-16
  Type: Initial release
  
• Version 1.1: 2015-04-29
  Changes: Other
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2024-03-20
  Changes: Data collection, Database references, Derived calculations