8BQ7 | pdb_00008bq7

Structure of the mouse 8-oxoguanine DNA Glycosylase mOGG1 in complex with ligand TH2829

• PDB DOI: https://doi.org/10.2210/pdb8BQ7/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-11-19 Released: 2023-11-29 
• Deposition Author(s): Scaletti, E., Stenmark, P.
• Funding Organization(s): Cancerfonden

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.307 (Depositor), 0.310 (DCC) 
• R-Value Work: 
  0.255 (Depositor), 0.260 (DCC) 

Literature

Nucleobase catalysts for the enzymatic activation of 8-oxoguanine DNA glycosylase 1

Hank, E.C., D’Arcy-Evans, N.D., Scaletti, E.R., Benitez-Buelga, C., Wallner, O., Ortis, F., Zhou, K., Meng, L., del Prado, A., Calvo, P., Almlof, I., Wiita, E., Nierlin, K., Kosenina, S., Kramer, A., Eddershaw, A., Kehler, M., Long, M., Jemth, A.S., Dawson, H., Stewart, J., Dickey, A., Astorga, M.E., Varga, M., Homan, E.J., Scobie, M., Knapp, S., Sastre, L., Stenmark, P., de Vega, M., Helleday, T., Michel, M.

(2025) RSC Chem Biol 

• DOI: https://doi.org/10.1039/D4CB00323C

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 107.83 kDa 
• Atom Count: 7,047 
• Modeled Residue Count: 913 
• Deposited Residue Count: 954 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
N-glycosylase/DNA lyase	A, B, C	318	Mus musculus	Mutation(s): 0  Gene Names: Ogg1 EC: 3.2.2 (PDB Primary Data), 4.2.99.18 (PDB Primary Data)
UniProt
Find proteins for O08760 (Mus musculus) Explore O08760  Go to UniProtKB:  O08760

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
R4U (Subject of Investigation/LOI)	D [auth A]	~{N}4-cyclohexyl-2~{H}-pyrazolo[3,4-d]pyrimidine-4,6-diamine C11 H16 N6 IQIULFHBHXKBGP-UHFFFAOYSA-N
GOL	F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NI	E [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.307 (Depositor), 0.310 (DCC) 
• R-Value Work:  0.255 (Depositor), 0.260 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.733	α = 90
b = 82.095	β = 90
c = 169.487	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-11-29 
Deposition Author(s): Scaletti, E., Stenmark, P.

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Funding Organization	Location	Grant Number
Cancerfonden	Sweden	--

Revision History  

• Version 1.0: 2023-11-29
  Type: Initial release
  
• Version 1.1: 2025-11-12
  Changes: Database references, Structure summary