7MZ4 | pdb_00007mz4

Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP

• PDB DOI: https://doi.org/10.2210/pdb7MZ4/pdb
• NAKB: 7MZ4

• Classification: TRANSFERASE/DNA
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-05-24 Released: 2022-06-01 
• Deposition Author(s): Koag, M.-C., Lee, S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.219 (Depositor) 

Starting Model: experimental

Literature

Structure of human DNA polymerase beta complexed with 3-deaza-3-methyladenine (3dMeA) in the template base paired with incoming dTTP

Koag, M.-C., Lee, S.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 47.57 kDa 
• Atom Count: 3,432 
• Modelled Residue Count: 357 
• Deposited Residue Count: 360 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	329	Homo sapiens	Mutation(s): 0  Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data), 4.2.99.18 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746  Go to UniProtKB:  P06746
PHAROS:  P06746 GTEx:  ENSG00000070501

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*CP*CP*GP*AP*CP*(DZM)P*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	B [auth T]	16	Homo sapiens

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*A)-3')	C [auth P]	10	Homo sapiens

Entity ID: 4
Molecule	Chains	Length	Organism	Image
DNA (5'-D(P*GP*TP*CP*GP*G)-3')	D	5	Homo sapiens

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
1FZ (Subject of Investigation/LOI)	I [auth A]	5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]thymidine C10 H18 N3 O13 P3 YRKUYVYMPXAOAT-XLPZGREQSA-N
MG (Subject of Investigation/LOI)	E [auth A], F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA (Subject of Investigation/LOI)	G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.270 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.216 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.219 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.706	α = 90
b = 80.183	β = 108.64
c = 54.927	γ = 90

Software Package:

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Koag, M.-C., Lee, S.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)	United States	ES-26676

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description