4MFA

Structure of human DNA polymerase beta complexed with nicked DNA containing a mismatched template O6MG and incoming TTP

PDB DOI: https://doi.org/10.2210/pdb4MFA/pdb
NAKB: 4MFA

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

Deposited: 2013-08-27 Released: 2014-08-27
Deposition Author(s): Koag, M.C., Min, K., Monzingo, A.F., Lee, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.283
R-Value Work: 0.212
R-Value Observed: 0.215

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structures of human DNA polymerase beta inserting bases opposite templating O6MG

Koag, M.C., Min, K., Monzingo, A.F., Lee, S.

To be published.

Macromolecule Content

Total Structure Weight: 47.05 kDa
Atom Count: 3,284
Modelled Residue Count: 353
Deposited Residue Count: 357
Unique protein chains: 1
Unique nucleic acid chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	325	Homo sapiens	Mutation(s): 0 Gene Names: POLB EC: 2.7.7.7 (PDB Primary Data), 4.2.99 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P06746 (Homo sapiens) Explore P06746 Go to UniProtKB: P06746
PHAROS: P06746
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P06746
Protein Feature View Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Length	Organism	Image
template	B [auth T]	16	N/A
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Reference Sequence

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Entity ID: 3
Molecule	Chains	Length	Organism	Image
up primer	C [auth P]	11	N/A
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Reference Sequence

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Entity ID: 4
Molecule	Chains	Length	Organism	Image
dn primer	D	5	N/A
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A]	H [auth A]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Ligand Interaction
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain I [auth P] MOL2 format, chain F [auth A] MOL2 format, chain I [auth P]	F [auth A], I [auth P]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Ligand Interaction
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A]	E [auth A], G [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.27 Å
R-Value Free: 0.283
R-Value Work: 0.212
R-Value Observed: 0.215
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.971	α = 90
b = 79.662	β = 106.68
c = 55.001	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
DENZO	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

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Entry History

Deposition Data

Released Date: 2014-08-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-27
Type: Initial release

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.