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), 0.230 (DCC)
R-Value Work:
0.199 (Depositor), 0.200 (DCC)
R-Value Observed:
0.201 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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 | 3D Structure

Entity ID: 1
Molecule	Chains	Length	Organism	Image
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 Z [auth E] SDF format, chain Y [auth E] SDF format, chain X [auth E] SDF format, chain W [auth D] SDF format, chain V [auth D] SDF format, chain R [auth C] SDF format, chain Q [auth C] SDF format, chain P [auth C] SDF format, chain O [auth B] SDF format, chain N [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth H] SDF format, chain I [auth A] SDF format, chain HA [auth H] SDF format, chain EA [auth G] SDF format, chain DA [auth G] SDF format, chain CA [auth G] SDF format, chain BA [auth F] SDF format, chain AA [auth F] MOL2 format, chain Z [auth E] MOL2 format, chain Y [auth E] MOL2 format, chain X [auth E] MOL2 format, chain W [auth D] MOL2 format, chain V [auth D] MOL2 format, chain R [auth C] MOL2 format, chain Q [auth C] MOL2 format, chain P [auth C] MOL2 format, chain O [auth B] MOL2 format, chain N [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain I [auth A] MOL2 format, chain HA [auth H] MOL2 format, chain EA [auth G] MOL2 format, chain DA [auth G] MOL2 format, chain CA [auth G] MOL2 format, chain BA [auth F] MOL2 format, chain AA [auth F] mmCIF format, chain Z [auth E] mmCIF format, chain Y [auth E] mmCIF format, chain X [auth E] mmCIF format, chain W [auth D] mmCIF format, chain V [auth D] mmCIF format, chain R [auth C] mmCIF format, chain Q [auth C] mmCIF format, chain P [auth C] mmCIF format, chain O [auth B] mmCIF format, chain N [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain I [auth A] mmCIF format, chain HA [auth H] mmCIF format, chain EA [auth G] mmCIF format, chain DA [auth G] mmCIF format, chain CA [auth G] mmCIF format, chain BA [auth F] mmCIF format, chain AA [auth F]	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 U [auth C] SDF format, chain T [auth C] SDF format, chain S [auth C] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain GA [auth G] SDF format, chain FA [auth G] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain GA [auth G] MOL2 format, chain FA [auth G] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain GA [auth G] mmCIF format, chain FA [auth G]	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]