8P6B | pdb_00008p6b

Ruthenium complex bound to a modified human telomeric sequence giving an antiparallel G-quadruplex

• PDB DOI: https://doi.org/10.2210/pdb8P6B/pdb
• NAKB: 8P6B

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


• Deposited: 2023-05-25 Released: 2024-06-12 
• Deposition Author(s): McQuaid, K.T., Cardin, C.J.
• Funding Organization(s): Biotechnology and Biological Sciences Research Council (BBSRC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.273 (Depositor), 0.315 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.359 (DCC) 

Literature

Ruthenium complex bound to an antiparallel G-quadruplex

McQuaid, K.T., Cardin, C.J.

To be published.

Biological Assembly 1  

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

Macromolecule Content 

• Total Structure Weight: 7.61 kDa 
• Atom Count: 504 
• Modeled Residue Count: 21 
• Deposited Residue Count: 21 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*GP*GP*TP*TP*TP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')	A	21	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0K8 (Subject of Investigation/LOI)	B [auth A]	Ruthenium bis-(phenanthroline) 12,17-dihydro-naphthodipyridophenazine-12,17-dione C50 H28 N8 O2 Ru LEJPQQFNZLHEQD-UHFFFAOYSA-N
K	C [auth A], D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.273 (Depositor), 0.315 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.359 (DCC) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 29.131	α = 90
b = 29.131	β = 90
c = 143.294	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
DIALS	data scaling
DIALS	data reduction
SHELXD	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2024-06-12 
Deposition Author(s): McQuaid, K.T., Cardin, C.J.

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Funding Organization	Location	Grant Number
Biotechnology and Biological Sciences Research Council (BBSRC)	United Kingdom	BB/T008342/1

Revision History  

• Version 1.0: 2024-06-12
  Type: Initial release
  
• Version 2.0: 2026-04-22
  Type: Coordinate replacement
  Reason: Polymer geometry
  Changes: Atomic model, Data collection, Derived calculations, Refinement description, Structure summary