8BAF | pdb_00008baf

Non-canonical quadruplex containing the oxidation product 8-oxoguanine

PDB DOI: https://doi.org/10.2210/pdb8BAF/pdb
NAKB: 8BAF

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: 1.60 Å
R-Value Free:
0.197 (Depositor), 0.200 (DCC)
R-Value Work:
0.186 (Depositor), 0.200 (DCC)
R-Value Observed:
0.187 (Depositor)

wwPDB Validation 3D Report Full Report

This is version 1.0 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: 4.9 kDa
Atom Count: 357
Modeled Residue Count: 14
Deposited Residue Count: 14
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((8OG)PCPAPTPGPCP*T)-3')	A, B	7	synthetic construct
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NCO Query on NCO Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain F [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [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]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.60 Å
R-Value Free: 0.197 (Depositor), 0.200 (DCC)
R-Value Work: 0.186 (Depositor), 0.200 (DCC)
R-Value Observed: 0.187 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 22.035	α = 90
b = 58.846	β = 90
c = 45.488	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

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

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.