9FXN

Human mitochondrial nuclease EXOG (hEXOG)

• PDB DOI: https://doi.org/10.2210/pdb9FXN/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-02 Released: 2024-07-31 
• Deposition Author(s): Karasinska, J.M., Szymanski, M.R.
• Funding Organization(s): European Research Council (ERC), European Molecular Biology Organization (EMBO)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.228 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 

Starting Model: experimental

Literature

Human mitochondrial nuclease EXOG (hEXOG)

Karasinska, J.M., Szymanski, M.R.

(2017) Nat Commun 8: 14959

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 72.73 kDa 
• Atom Count: 5,089 
• Modelled Residue Count: 601 
• Deposited Residue Count: 634 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease EXOG, mitochondrial	A, B	317	Homo sapiens	Mutation(s): 0  Gene Names: EXOG, ENDOGL1, ENDOGL2, ENGL EC: 3.1.30
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2C4 (Homo sapiens) Explore Q9Y2C4  Go to UniProtKB:  Q9Y2C4
PHAROS:  Q9Y2C4 GTEx:  ENSG00000157036

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG (Subject of Investigation/LOI)	C [auth A], D [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.62 Å
• R-Value Free: 0.228 
• R-Value Work: 0.157 
• R-Value Observed: 0.159 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.55	α = 90
b = 83.56	β = 113.51
c = 74.39	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-07-31 
Deposition Author(s): Karasinska, J.M., Szymanski, M.R.

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Funding Organization	Location	Grant Number
European Research Council (ERC)	European Union	--
European Molecular Biology Organization (EMBO)	European Union	--

Revision History  

• Version 1.0: 2024-07-31
  Type: Initial release