Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Macromolecule Content

• Total Structure Weight: 11.77 kDa 
• Atom Count: 858 
• Modelled Residue Count: 28 
• Deposited Residue Count: 28 
• Unique nucleic acid chains: 1

6RNL

L-[Ru(TAP)2(dppz)]2+ bound to the G-quadruplex forming sequence d(TAGGGTT)

• PDB DOI: 10.2210/pdb6RNL/pdb
• NDB: 6RNL

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


• Deposited: 2019-05-09 Released: 2019-08-28 
• 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: 1.88 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Three thymine/adenine binding modes of the ruthenium complex Lambda-[Ru(TAP)2(dppz)]2+to the G-quadruplex forming sequence d(TAGGGTT) shown by X-ray crystallography.

McQuaid, K., Hall, J.P., Baumgaertner, L., Cardin, D.J., Cardin, C.J.

(2019) Chem Commun (Camb) 55: 9116-9119

• PubMed: 31298665 
• DOI: 10.1039/c9cc04316k
• Primary Citation of Related Structures:  
  6RNL


• PubMed Abstract: 
  

Λ-[Ru(TAP)2(dppz)]2+ was crystallised with the G-quadruplex-forming heptamer d(TAGGGTT). Surprisingly, even though there are four unique binding sites, the complex is not in contact with any G-quartet surface. Two complexes stabilise cavities formed from terminal T·A and T·T mismatched pairs. A third shows kinking by a TAP ligand between T·T linkages, while the fourth shows sandwiching of a dppz ligand between a T·A/T·A quadruplex and a T·T mismatch, stabilised by an additional T·A base pair stacking interaction on a TAP surface. Overall, the structure shows an unexpected affinity for thymine, and suggests models for G-quadruplex loop binding.

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Organizational Affiliation: 

Department of Chemistry, University of Reading, Whiteknights, Reading, RG6 6AD, UK. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*TP*AP*GP*GP*GP*TP*T)-3')	A, B, C, D	7	synthetic construct

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RKL (Subject of Investigation/LOI)	F [auth A], G [auth A], J [auth C], K [auth D]	Ru(tap)2(dppz) complex C38 H22 N12 Ru PIKVAZQLFXBUSD-UHFFFAOYSA-N
K	E [auth A], I [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
NA	H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 0.214 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.514	α = 90
b = 38.514	β = 90
c = 128.804	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data reduction
DIALS	data scaling
SHELXDE	phasing
xia2	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2019-05-09 
• Released Date: 2019-08-28 
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: 2019-08-28
  Type: Initial release
  
• Version 1.1: 2019-09-11
  Changes: Data collection, Database references