8OE8 | pdb_00008oe8

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

PDB DOI: https://doi.org/10.2210/pdb8OE8/pdb
NAKB: 8OE8

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: 1.30 Å
R-Value Free:
0.209 (Depositor), 0.205 (DCC)
R-Value Work:
0.169 (Depositor), 0.165 (DCC)
R-Value Observed:
0.171 (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: 16.02 kDa
Atom Count: 1,375
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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SPM Query on SPM Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain O [auth C] SDF format, chain T [auth E] SDF format, chain X [auth G] MOL2 format, chain K [auth A] MOL2 format, chain O [auth C] MOL2 format, chain T [auth E] MOL2 format, chain X [auth G] mmCIF format, chain K [auth A] mmCIF format, chain O [auth C] mmCIF format, chain T [auth E] mmCIF format, chain X [auth G]	K [auth A], O [auth C], T [auth E], X [auth G]	SPERMINE C₁₀ H₂₆ N₄ PFNFFQXMRSDOHW-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain O [auth C] Focus chain T [auth E] Focus chain X [auth G] Interactions & Density Focus chain K [auth A] Focus chain O [auth C] Focus chain T [auth E] Focus chain X [auth G]
CU (Subject of Investigation/LOI) Query on CU Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain L [auth C] SDF format, chain Q [auth E] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain U [auth G] SDF format, chain V [auth G] SDF format, chain W [auth G] SDF format, chain N [auth C] SDF format, chain M [auth C] SDF format, chain J [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth C] MOL2 format, chain Q [auth E] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain U [auth G] MOL2 format, chain V [auth G] MOL2 format, chain W [auth G] MOL2 format, chain N [auth C] MOL2 format, chain M [auth C] MOL2 format, chain J [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth C] mmCIF format, chain Q [auth E] mmCIF format, chain R [auth E] mmCIF format, chain S [auth E] mmCIF format, chain U [auth G] mmCIF format, chain V [auth G] mmCIF format, chain W [auth G] mmCIF format, chain N [auth C] mmCIF format, chain M [auth C] mmCIF format, chain J [auth A]	I [auth A] J [auth A] L [auth C] M [auth C] N [auth C] I [auth A], J [auth A], L [auth C], M [auth C], N [auth C], Q [auth E], R [auth E], S [auth E], U [auth G], V [auth G], W [auth G]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G] Interactions & Density Focus chain I [auth A] Focus chain J [auth A] Focus chain L [auth C] Focus chain M [auth C] Focus chain N [auth C] Focus chain Q [auth E] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth G] Focus chain V [auth G] Focus chain W [auth G]
PEO (Subject of Investigation/LOI) Query on PEO Download Ideal Coordinates CCD File SDF format, chain P [auth C] MOL2 format, chain P [auth C] mmCIF format, chain P [auth C]	P [auth C]	HYDROGEN PEROXIDE H₂ O₂ MHAJPDPJQMAIIY-UHFFFAOYSA-N		Interactions Focus chain P [auth C] Interactions & Density Focus chain P [auth C]