6XCL | pdb_00006xcl

Crystal Structure of human telomeric DNA G-quadruplex in complex with a novel platinum(II) complex.

• PDB DOI: https://doi.org/10.2210/pdb6XCL/pdb
• NAKB: 6XCL

• Classification: DNA
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2020-06-08 Released: 2020-11-04 
• Deposition Author(s): Miron, C.E., van Staalduinen, L.M., Jia, Z., Petitjean, A.
• Funding Organization(s): Natural Sciences and Engineering Research Council (NSERC, Canada)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Going Platinum to the Tune of a Remarkable Guanine Quadruplex Binder: Solution- and Solid-State Investigations.

Miron, C.E., van Staalduinen, L., Rangaswamy, A.M., Chen, M., Liang, Y., Jia, Z., Mergny, J.L., Petitjean, A.

(2021) Angew Chem Int Ed Engl 60: 2500-2507

• PubMed: 33090592 
• DOI: https://doi.org/10.1002/anie.202012520
• Primary Citation Related Structures: 
  6XCL


• PubMed Abstract: 
  

  Guanine quadruplex recognition has gained increasing attention, inspired by the growing awareness of the key roles played by these non-canonical nucleic acid architectures in cellular regulatory processes. We report here the solution and solid-state studies of a novel planar platinum(II) complex that is easily assembled from a simple ligand, and exhibits notable binding affinity for guanine quadruplex structures, while maintaining good selectivity for guanine quadruplex over duplex structures. A crystal structure of this ligand complexed with a telomeric quadruplex confirms double end-capping, with dimerization at the 5' interface.

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Organizational Affiliation: 
• Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, ON, K7L 3N6, Canada.
Department of Biomedical and Molecular Sciences, Queen's University, Kingston, ON, K7L 3N6, Canada.
Inserm U1212/CNRS UMR5320/Université de Bordeaux, Institut Européen de Chimie et Biologie, 2 rue Escarpit, 33607, Pessac, France.
Laboratoire d'Optique et Biosciences, École Polytechnique, CNRS, INSERM, Institut Polytechnique de Paris, 91128, Palaiseau cedex, France.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 16.05 kDa 
• Atom Count: 1,042 
• Modeled Residue Count: 44 
• Deposited Residue Count: 44 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*GP*TP*TP*AP*GP*GP*G)-3')	A, B	22	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
V4A (Subject of Investigation/LOI)	C [auth A], E [auth A], K [auth B]	Platinum(II) bis[3-(pyridin-2-yl)-[1,2,4]triazolo[4,3-a]pyridine] C22 H16 N8 Pt RJNZXUGUJQBFMV-UHFFFAOYSA-N
EDO	D [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	F [auth A], G [auth A], H [auth A], J [auth B], L [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.243 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.03	α = 90
b = 64.03	β = 90
c = 42.23	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
MxDC	data collection
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-11-04 
Deposition Author(s): Miron, C.E., van Staalduinen, L.M., Jia, Z., Petitjean, A.

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Funding Organization	Location	Grant Number
Natural Sciences and Engineering Research Council (NSERC, Canada)	Canada	315311-2013

Revision History  

• Version 1.0: 2020-11-04
  Type: Initial release
  
• Version 1.1: 2021-02-03
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Database references, Refinement description