8OEC | pdb_00008oec

Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for another 30 minutes, third collection at room temperature

• PDB DOI: https://doi.org/10.2210/pdb8OEC/pdb
• NAKB: 8OEC

• 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: 2.10 Å
• R-Value Free: 
  0.188 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.149 (Depositor) 

Starting Model: experimental

Literature

Structural analysis of peroxide-soaked DNA crystals containing ordered copper binding sites: towards understanding oxidative damage at the atomic scale

Lambert, M.C., Hall, J.P.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 3.89 kDa 
• Atom Count: 305 
• Modeled Residue Count: 12 
• Deposited Residue Count: 12 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')	A, B	6	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SPM	C [auth A]	SPERMINE C10 H26 N4 PFNFFQXMRSDOHW-UHFFFAOYSA-N
CU (Subject of Investigation/LOI)	D [auth A]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.188 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.147 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.149 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.355	α = 90
b = 30.778	β = 90
c = 43.104	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
CrysalisPro	data reduction
CrysalisPro	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