8BAG | pdb_00008bag

Copper(II) bound to a non-canonical quadruplex containing the damaged base 8-oxoguanine

PDB DOI: https://doi.org/10.2210/pdb8BAG/pdb
NAKB: 8BAG

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

Deposited: 2022-10-11 Released: 2023-10-25
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: 1.13 Å
R-Value Free:
0.172 (Depositor), 0.196 (DCC)
R-Value Work:
0.152 (Depositor)
R-Value Observed:
0.153 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8BAG

This is version 1.1 of the entry. See complete history.

Literature

Oxidative damage induce copper(II)-DNA binding

Lambert, M.C., Brazier, J.A., Cardin, C.J., Hall, J.P.

To be published.

Macromolecule Content

Total Structure Weight: 5.03 kDa
Atom Count: 370
Modeled Residue Count: 14
Deposited Residue Count: 14
Unique nucleic acid chains: 1

Macromolecules

Find similar nucleic acids by: Sequence

Molecule	Chains	Length	Organism	Image
Entity ID: 1
DNA (5'-D((8OG)PCPAPTPGPCP*T)-3')	A, B	7	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCO Query on NCO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A], D [auth A], E [auth A], F [auth A]	COBALT HEXAMMINE(III) Co H₁₈ N₆ DYLMFCCYOUSRTK-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A]
CU (Subject of Investigation/LOI) Query on CU Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain G [auth A] mmCIF format, chain H [auth B] mmCIF format, chain G [auth A]	G [auth A], H [auth B]	COPPER (II) ION Cu JPVYNHNXODAKFH-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Interactions & Density Focus chain G [auth A] Focus chain H [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.13 Å
R-Value Free: 0.172 (Depositor), 0.196 (DCC)
R-Value Work: 0.152 (Depositor)
R-Value Observed: 0.153 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 21.99	α = 90
b = 58.87	β = 90
c = 45.46	γ = 90

Software Package:

Software Name	Purpose
xia2	data scaling
XDS	data reduction
PHASER	phasing
Coot	model building
PHENIX	refinement

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2023-10-25

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: 2023-10-25
Type: Initial release
Version 1.1: 2026-03-04
Changes: Refinement description, Structure summary

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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.