7R6V

Human EXOG complexed with dRP-containing DNA

• PDB DOI: https://doi.org/10.2210/pdb7R6V/pdb
• NAKB: 7R6V

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-06-23 Released: 2022-08-24 
• Deposition Author(s): Szymanski, M.R., Yin, Y.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.240 
• R-Value Work: 0.200 

Literature

Human EXOG possesses strong AP hydrolysis activity

Szymanski, M.R., Yin, Y.W.

To be published.

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 169.35 kDa 
• Atom Count: 11,230 
• Modelled Residue Count: 1,237 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclease EXOG, mitochondrial	A [auth D], B [auth E], G, H [auth I]	311	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

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*TP*GP*AP*CP*GP*TP*GP*CP*G)-3')	C [auth F], D [auth H], I [auth J], J [auth K]	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*AP*A)-3')	E [auth B], F [auth A], K [auth L], L [auth M]	12	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	N [auth D], Q [auth G], T [auth I]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG (Subject of Investigation/LOI)	M [auth D], O [auth F], P [auth H], R [auth I], S [auth I], U [auth J]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.16 Å
• R-Value Free: 0.240 
• R-Value Work: 0.200 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.749	α = 69.05
b = 79.085	β = 65.02
c = 79.635	γ = 89.72

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-08-24 
Deposition Author(s): Szymanski, M.R., Yin, Y.W.

Revision History  

• Version 1.0: 2022-08-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description