5LFX

Lambda-[Ru(phen)2(dppz-11,12-Me)]2+ bound to a short substituted DNA sequence

• PDB DOI: https://doi.org/10.2210/pdb5LFX/pdb
• NAKB: 5LFX

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


• Deposited: 2016-07-04 Released: 2017-02-15 
• 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: 1.56 Å
• R-Value Free: 
  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 
  0.146 (Depositor) 

Literature

Guanine Can Direct Binding Specificity of Ru-dipyridophenazine (dppz) Complexes to DNA through Steric Effects.

Hall, J.P., Gurung, S.P., Henle, J., Poidl, P., Andersson, J., Lincoln, P., Winter, G., Sorensen, T., Cardin, D.J., Brazier, J.A., Cardin, C.J.

(2017) Chemistry 23: 4981-4985

• PubMed: 28105682 
• DOI: https://doi.org/10.1002/chem.201605508
• Primary Citation of Related Structures:  
  5LFS, 5LFW, 5LFX


• PubMed Abstract: 
  

  X-ray crystal structures of three Λ-[Ru(L) ₂ dppz] ²⁺ complexes (dppz=dipyridophenazine; L=1,10-phenanthroline (phen), 2,2'-bipyridine (bpy)) bound to d((5BrC)GGC/GCCG) showed the compounds intercalated at a 5'-CG-3' step. The compounds bind through canted intercalation, with the binding angle determined by the guanine NH ₂ group, in contrast to symmetrical intercalation previously observed at 5'-TA-3' sites. This result suggests that canted intercalation is preferred at 5'-CG-3' sites even though the site itself is symmetrical, and we hypothesise that symmetrical intercalation in a 5'-CG-3' step could give rise to a longer luminescence lifetime than canted intercalation.

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Organizational Affiliation: 

Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK.

Biological Assembly 1  

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 3.29 kDa 
• Atom Count: 262 
• Modelled Residue Count: 8 
• Deposited Residue Count: 8 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*CP*G)-3')	A	4	synthetic construct

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*(CBR)P*GP*GP*C)-3')	B [auth C]	4	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9ZQ	D [auth A]	Ru(phen)2(dppz-11,12-Me2) C44 H30 N8 Ru SWTHIMQOVCZKDV-UHFFFAOYSA-N
BA	C [auth A]	BARIUM ION Ba XDFCIPNJCBUZJN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.56 Å
• R-Value Free:  0.192 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.144 (Depositor), 0.150 (DCC) 
• R-Value Observed: 0.146 (Depositor) 

Space Group: P 6₄ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.72	α = 90
b = 67.72	β = 90
c = 35.85	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
SHELXCD	phasing
xia2	data reduction

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2017-02-15 
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
Biotechnology and Biological Sciences Research Council	United Kingdom	BB/M006435/1

Revision History  

• Version 1.0: 2017-02-15
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Database references
• Version 1.2: 2017-08-30
  Changes: Author supporting evidence
• Version 2.0: 2024-05-08
  Changes: Atomic model, Data collection, Database references, Derived calculations