2PXI

Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate

• PDB DOI: https://doi.org/10.2210/pdb2PXI/pdb
• NAKB: 2PXI

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


• Deposited: 2007-05-14 Released: 2008-01-08 
• Deposition Author(s): McKenna, C.E., Batra, V.K., Beard, W.A., Pedersen, L.C., Wilson, S.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.270 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 

Starting Model: experimental

Literature

(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta.

McKenna, C.E., Kashemirov, B.A., Upton, T.G., Batra, V.K., Goodman, M.F., Pedersen, L.C., Beard, W.A., Wilson, S.H.

(2007) J Am Chem Soc 129: 15412-15413

• PubMed: 18031037 
• DOI: https://doi.org/10.1021/ja072127v
• Primary Citation of Related Structures:  
  2PXI

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Organizational Affiliation: 

Department of Chemistry, University of Southern California, Los Angeles, California 90089, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 48.45 kDa 
• Atom Count: 3,624 
• Modelled Residue Count: 357 
• Deposited Residue Count: 366 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	D [auth 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: 1
Molecule	Chains	Length	Organism	Image
5'-D(*CP*CP*GP*AP*CP*CP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3'	A [auth T]	16	N/A

Entity ID: 2
Molecule	Chains	Length	Organism	Image
5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3'	B [auth P]	10	N/A

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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GFH	N [auth A]	2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE C11 H17 F N5 O12 P3 PVDLZOAYDIZEDJ-AVAJSQPUSA-N
CL	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA	F [auth A], G [auth A], H [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.270 
• R-Value Work: 0.206 
• R-Value Observed: 0.206 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.6	α = 90
b = 80.2	β = 107.8
c = 55.4	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-01-08 
Deposition Author(s): McKenna, C.E., Batra, V.K., Beard, W.A., Pedersen, L.C., Wilson, S.H.

Revision History  

• Version 1.0: 2008-01-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description