7MZ0 | pdb_00007mz0

Structure of human DNA polymerase beta complexed with dzA as the template base in a 1-nucleotide gapped DNA

• PDB DOI: https://doi.org/10.2210/pdb7MZ0/pdb
• NAKB: 7MZ0

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


• Deposited: 2021-05-23 Released: 2022-05-25 
• Deposition Author(s): Koag, M.-C., Lee, S.
• Funding Organization(s): National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free: 
  0.276 (Depositor), 0.272 (DCC) 
• R-Value Work: 
  0.221 (Depositor), 0.225 (DCC) 
• R-Value Observed: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Structure Of Human Dna Polymerase Beta Complexed With dzA As The Template Base In A 1-Nucleotide Gapped Dna

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: 47.03 kDa 
• Atom Count: 3,395 
• Modeled Residue Count: 358 
• 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*(4DU)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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NA (Subject of Investigation/LOI)	E [auth A], F [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.02 Å
• R-Value Free:  0.276 (Depositor), 0.272 (DCC) 
• R-Value Work:  0.221 (Depositor), 0.225 (DCC) 
• R-Value Observed: 0.224 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.649	α = 90
b = 79.172	β = 106.27
c = 54.819	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: 2022-05-25 
Deposition Author(s): Koag, M.-C., Lee, S.

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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: 2022-05-25
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Refinement description