PDBsum entry 2pxi

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protein dna_rna ligands metals links
Lyase, transferase/DNA PDB id
Jmol PyMol
Protein chain
326 a.a. *
_NA ×3
_CL ×5
Waters ×321
* Residue conservation analysis
PDB id:
Name: Lyase, transferase/DNA
Title: Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma- monofluoromethylene triphosphate
Structure: DNA polymerase beta. Chain: a. Engineered: yes. 5'- d( Cp Cp Gp Ap Cp Cp Gp Cp Gp Cp Ap Tp Cp Ap Gp C)-3'. Chain: t. Engineered: yes. 5'-d( Gp Cp Tp Gp Ap Tp Gp Cp Gp (Doc))-3'. Chain: p.
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: polb. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Synthetic: yes
2.10Å     R-factor:   0.206     R-free:   0.270
Authors: C.E.Mckenna,V.K.Batra,W.A.Beard,L.C.Pedersen,S.H.Wilson
Key ref: C.E.McKenna et al. (2007). (R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta. J Am Chem Soc, 129, 15412-15413. PubMed id: 18031037
14-May-07     Release date:   08-Jan-08    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
P06746  (DPOLB_HUMAN) -  DNA polymerase beta
335 a.a.
326 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   6 terms 
  Biological process     immunoglobulin heavy chain V-D-J recombination   27 terms 
  Biochemical function     protein binding     12 terms  


J Am Chem Soc 129:15412-15413 (2007)
PubMed id: 18031037  
(R)-beta,gamma-fluoromethylene-dGTP-DNA ternary complex with DNA polymerase beta.
C.E.McKenna, B.A.Kashemirov, T.G.Upton, V.K.Batra, M.F.Goodman, L.C.Pedersen, W.A.Beard, S.H.Wilson.
No abstract given.


Literature references that cite this PDB file's key reference

  PubMed id Reference
21117131 C.Dalvit, and A.Vulpetti (2011).
Fluorine-protein interactions and ¹⁹F NMR isotropic chemical shifts: An empirical correlation with implications for drug design.
  ChemMedChem, 6, 104-114.  
20724659 G.K.Surya Prakash, M.Zibinsky, T.G.Upton, B.A.Kashemirov, C.E.McKenna, K.Oertell, M.F.Goodman, V.K.Batra, L.C.Pedersen, W.A.Beard, D.D.Shock, S.H.Wilson, and G.A.Olah (2010).
Synthesis and biological evaluation of fluorinated deoxynucleotide analogs based on bis-(difluoromethylene)triphosphoric acid.
  Proc Natl Acad Sci U S A, 107, 15693-15698.
PDB code: 3lk9
19850352 E.Gaidamauskas, H.Parker, B.A.Kashemirov, A.A.Holder, K.Saejueng, C.E.McKenna, and D.C.Crans (2009).
Complexation of bisphosphonates with ytterbium(III): application of phosphate and ATP detection assay based on Yb(3+)-pyrocatechol violet.
  J Inorg Biochem, 103, 1652-1657.  
19391628 S.C.Kamerlin, C.E.McKenna, M.F.Goodman, M.F.Goondman, and A.Warshel (2009).
A computational study of the hydrolysis of dGTP analogues with halomethylene-modified leaving groups in solution: implications for the mechanism of DNA polymerases.
  Biochemistry, 48, 5963-5971.  
18811136 F.Liang, N.Jain, T.Hutchens, D.D.Shock, W.A.Beard, S.H.Wilson, M.P.Chiarelli, and B.P.Cho (2008).
Alpha,beta-methylene-2'-deoxynucleoside 5'-triphosphates as noncleavable substrates for DNA polymerases: isolation, characterization, and stability studies of novel 2'-deoxycyclonucleosides, 3,5'-cyclo-dG, and 2,5'-cyclo-dT.
  J Med Chem, 51, 6460-6470.  
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