8OE7 | pdb_00008oe7

Crystal structure of the Z-DNA duplex d(CGCGCG) containing ordered copper(II) and soaked in hydrogen peroxide for 5 minutes

PDB DOI: https://doi.org/10.2210/pdb8OE7/pdb
NAKB: 8OE7

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.233 (Depositor), 0.233 (DCC)
R-Value Work:
0.199 (Depositor), 0.198 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8OE7

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.

Macromolecule Content

Total Structure Weight: 15.99 kDa
Atom Count: 1,290
Modeled Residue Count: 48
Deposited Residue Count: 48
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D(CPGPCPGPCPG)-3')	A, B, C, D, E A, B, C, D, E, F, G, H	6	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain AA [auth F] SDF format, chain BA [auth F] SDF format, chain CA [auth G] SDF format, chain DA [auth G] SDF format, chain EA [auth G] SDF format, chain HA [auth H] SDF format, chain I [auth A] SDF format, chain IA [auth H] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth C] SDF format, chain Q [auth C] SDF format, chain R [auth C] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain X [auth E] SDF format, chain Y [auth E] SDF format, chain Z [auth E] SDF format, chain J [auth A] MOL2 format, chain AA [auth F] MOL2 format, chain BA [auth F] MOL2 format, chain CA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain HA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain R [auth C] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain X [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain Z [auth E] MOL2 format, chain J [auth A] mmCIF format, chain AA [auth F] mmCIF format, chain BA [auth F] mmCIF format, chain CA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain HA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain R [auth C] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain X [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain Z [auth E] mmCIF format, chain J [auth A]	AA [auth F] BA [auth F] CA [auth G] DA [auth G] EA [auth G] AA [auth F], BA [auth F], CA [auth G], DA [auth G], EA [auth G], HA [auth H], I [auth A], IA [auth H], J [auth A], K [auth A], N [auth B], O [auth B], P [auth C], Q [auth C], R [auth C], V [auth D], W [auth D], X [auth E], Y [auth E], Z [auth E]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E] Interactions & Density Focus chain AA [auth F] Focus chain BA [auth F] Focus chain CA [auth G] Focus chain DA [auth G] Focus chain EA [auth G] Focus chain HA [auth H] Focus chain I [auth A] Focus chain IA [auth H] Focus chain J [auth A] Focus chain K [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth C] Focus chain Q [auth C] Focus chain R [auth C] Focus chain V [auth D] Focus chain W [auth D] Focus chain X [auth E] Focus chain Y [auth E] Focus chain Z [auth E]
PEO (Subject of Investigation/LOI) Query on PEO Download:Ideal Coordinates CCD File SDF format, chain FA [auth G] SDF format, chain GA [auth G] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain U [auth C] MOL2 format, chain FA [auth G] MOL2 format, chain GA [auth G] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain U [auth C] mmCIF format, chain FA [auth G] mmCIF format, chain GA [auth G] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain U [auth C]	FA [auth G] GA [auth G] L [auth A] M [auth A] S [auth C] FA [auth G], GA [auth G], L [auth A], M [auth A], S [auth C], T [auth C], U [auth C]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain FA [auth G] Focus chain GA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C] Interactions & Density Focus chain FA [auth G] Focus chain GA [auth G] Focus chain L [auth A] Focus chain M [auth A] Focus chain S [auth C] Focus chain T [auth C] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.233 (Depositor), 0.233 (DCC)
R-Value Work: 0.199 (Depositor), 0.198 (DCC)
R-Value Observed: 0.201 (Depositor)

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 18.282	α = 90.01
b = 30.737	β = 89.95
c = 42.557	γ = 90.01

Software Package:

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

Structure Validation

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View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-03-27

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.