8OEX

Crystal structure of the native Z-DNA duplex d(CGCGCG) before soaking of CuCl2

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

  • Deposited: 2023-03-13 Released: 2024-03-27 
  • Deposition Author(s): Lambert, M.C., Hall, J.P.
  • Funding Organization(s): Engineering and Physical Sciences Research Council

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free: 
    0.125 (Depositor), 0.130 (DCC) 
  • R-Value Work: 
    0.105 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 
    0.106 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SPMClick on this verticalbar to view details

This is version 1.0 of the entry. See complete history


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.

Macromolecules

Find similar nucleic acids by:  Sequence   |   3D Structure  

Entity ID: 1
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*GP*CP*GP*CP*G)-3')
A, B
6synthetic construct
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SPM
Query on SPM

Download Ideal Coordinates CCD File 
C [auth A]SPERMINE
C10 H26 N4
PFNFFQXMRSDOHW-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.07 Å
  • R-Value Free:  0.125 (Depositor), 0.130 (DCC) 
  • R-Value Work:  0.105 (Depositor), 0.110 (DCC) 
  • R-Value Observed: 0.106 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 18.283α = 90
b = 30.764β = 90
c = 42.477γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
CrysalisProdata reduction
CrysalisProdata scaling
PHENIXphasing
Cootmodel building
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted SPMClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Engineering and Physical Sciences Research CouncilUnited Kingdom--

Revision History  (Full details and data files)

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