8OE3 | pdb_00008oe3

Crystal structure of the non-canonical quadruplex d(GCATGCT) before soaking

• PDB DOI: https://doi.org/10.2210/pdb8OE3/pdb
• NAKB: 8OE3

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


• Deposited: 2023-03-10 Released: 2024-03-27 
• Deposition Author(s): Lambert, M.C., Hall, J.P.
• Funding Organization(s): Engineering and Physical Sciences Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free: 
  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: experimental

Literature

Oxidative damage induce copper(II)-DNA binding

Lambert, M.C., Brazier, J.A., Cardin, C.J., Hall, J.P.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 5.19 kDa 
• Atom Count: 431 
• Modeled Residue Count: 14 
• Deposited Residue Count: 14 
• Unique nucleic acid chains: 1

Macromolecules

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NCO	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth B]	COBALT HEXAMMINE(III) Co H18 N6 DYLMFCCYOUSRTK-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.08 Å
• R-Value Free:  0.185 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.164 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.157	α = 90
b = 59.156	β = 90
c = 45.666	γ = 90

Software Package:

Software Name	Purpose
GDA	data collection
xia2	data reduction
DIALS	data scaling
PHENIX	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-03-27 
Deposition Author(s): Lambert, M.C., Hall, J.P.

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Funding Organization	Location	Grant Number
Engineering and Physical Sciences Research Council	United Kingdom	--

Revision History  

• Version 1.0: 2024-03-27
  Type: Initial release