3GDX

Dna polymerase beta with a gapped DND substrate and dTMP(CF2)PP

• PDB DOI: https://doi.org/10.2210/pdb3GDX/pdb
• NAKB: 3GDX

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


• Deposited: 2009-02-24 Released: 2009-05-05 
• Deposition Author(s): Wilson, S.H., Batra, V.K., Pedersen, L.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates: a convenient synthesis of useful probes for DNA polymerase beta structure and function

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

(2009) Org Lett 11: 1883-1886

• PubMed: 19351147 
• DOI: https://doi.org/10.1021/ol701755k
• Primary Citation of Related Structures:  
  3GDX


• PubMed Abstract: 
  

  Alpha,beta-difluoromethylene deoxynucleoside 5'-triphosphates (dNTPs, N = A or C) are advantageously obtained via phosphorylation of corresponding dNDP analogues using catalytic ATP, PEP, nucleoside diphosphate kinase, and pyruvate kinase. DNA pol beta K(d) values for the alpha,beta-CF(2) and unmodified dNTPs, alpha,beta-NH dUTP, and the alpha,beta-CH(2) analogues of dATP and dGTP are discussed in relation to the conformations of alpha,beta-CF(2) dTTP versus alpha,beta-NH dUTP bound into the enzyme active site.

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Organizational Affiliation: 

Department of Chemistry, University of Southern California, Los Angeles, California 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: 47.31 kDa 
• Atom Count: 3,601 
• Modelled Residue Count: 357 
• Deposited Residue Count: 357 
• Unique protein chains: 1
• Unique nucleic acid chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase beta	A	326	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
5'-D(*CP*CP*GP*AP*CP*AP*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
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
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
4BD	E [auth A]	5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]thymidine C11 H17 F2 N2 O13 P3 WQZXQECPJNOPSV-XLPZGREQSA-N
CL	J [auth A], K [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: 2.20 Å
• R-Value Free: 0.266 
• R-Value Work: 0.208 
• R-Value Observed: 0.208 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.5	α = 90
b = 79.7	β = 107.9
c = 55.3	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-05-05 
Deposition Author(s): Wilson, S.H., Batra, V.K., Pedersen, L.C.

Revision History  

• Version 1.0: 2009-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description