7R6T | pdb_00007r6t

Human EXOG complexed with dRP-containing DNA

• PDB DOI: https://doi.org/10.2210/pdb7R6T/pdb
• NAKB: 7R6T

• Classification: DNA BINDING PROTEIN/DNA
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• 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: 2.90 Å
• R-Value Free: 
  0.286 (Depositor), 0.284 (DCC) 
• R-Value Work: 
  0.229 (Depositor), 0.228 (DCC) 

Starting Model: experimental

Literature

Human EXOG possesses strong AP hydrolysis activity

Szymanski, M.R., Yin, Y.W.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: SAXS

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: 125.22 kDa 
• Atom Count: 7,809 
• Modeled Residue Count: 915 
• Deposited Residue Count: 996 
• 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], D [auth C], G [auth L]	311	Homo sapiens	Mutation(s): 1  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(3DR)P*CP*TP*GP*AP*CP*GP*TP*GP*C)-3')	B [auth F], E, H [auth M]	10	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*GP*CP*AP*CP*GP*TP*CP*AP*GP*A)-3')	C [auth A], F [auth B], I [auth K]	11	synthetic construct

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MG	J [auth F], K [auth A], L [auth E], N [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	M [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.286 (Depositor), 0.284 (DCC) 
• R-Value Work:  0.229 (Depositor), 0.228 (DCC) 

Space Group: P 2₁ 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 73.252	α = 90
b = 100.056	β = 90
c = 174.902	γ = 90

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
• Version 1.2: 2024-12-25
  Changes: Advisory, Derived calculations, Structure summary