3TFR

Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, b dAMP(CF2)PP in the active site

• PDB DOI: https://doi.org/10.2210/pdb3TFR/pdb
• NAKB: 3TFR

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


• Deposited: 2011-08-16 Released: 2012-03-21 
• Deposition Author(s): Chamberlain, B.T., Batra, V.K., Beard, W.A., Kadina, A.P., Shock, D.D., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.251 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.188 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta.

Chamberlain, B.T., Batra, V.K., Beard, W.A., Kadina, A.P., Shock, D.D., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

(2012) Chembiochem 13: 528-530

• PubMed: 22315190 
• DOI: https://doi.org/10.1002/cbic.201100738
• Primary Citation of Related Structures:  
  3TFR, 3TFS


• PubMed Abstract: 
  

  The influence of water: crystallization of (R/S)-α,β-CHF-dATP with the preorganized pol β-DNA complex shows that (S)-α,β-CHF-dATP is preferentially bound to the active site with the C=F fluorine proximal to a structural water bound to Asp276.

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Organizational Affiliation: 

Departments of Chemistry and Biology, University of Southern California, Los Angeles, CA 90089, USA.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 48.44 kDa 
• Atom Count: 3,764 
• Modelled Residue Count: 357 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	335	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*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')	B [auth T]	16	N/A

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

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F3A	E [auth A]	2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine C11 H16 F2 N5 O11 P3 SRDWTQAPDNVDMA-RRKCRQDMSA-N
CL	J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	H [auth A], I [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.251 (Depositor), 0.230 (DCC) 
• R-Value Work:  0.188 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.89	α = 90
b = 79.38	β = 107.64
c = 55.65	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Chamberlain, B.T., Batra, V.K., Beard, W.A., Kadina, A.P., Shock, D.D., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description