Brand  (β version)

PDB ID: 3C2L

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Ligands
Code Name Style Show Link
F2A 2'-deoxy-5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]adenosine PoSSuM
MN Manganese (II) ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
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Structure summary

Code : 3C2L   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Ternary complex of DNA POLYMERASE BETA with a C:DAPCPP mismatch in the active site
Release Data : 2008-05-20
Compound :
mol_id molecule chains
1 DNA (5'-D(*DCP*DCP*DGP*DAP*DCP*DCP*DGP*DCP*DGP*DCP*DAP*DTP*DCP*DAP*DGP*DC)-3') T
mol_id molecule chains
2 DNA (5'-D(*DGP*DCP*DTP*DGP*DAP*DTP*DGP*DCP*DGP*DC)-3') P
mol_id molecule chains
3 DNA (5'-D(P*DGP*DTP*DCP*DGP*DG)-3') D
mol_id molecule chains
4 DNA polymerase beta A
ec: 2.7.7.7, 4.2.99.-
Source :
mol_id organism_scientific
1
synthetic: yes
mol_id organism_scientific
2
synthetic: yes
mol_id organism_scientific
3
synthetic: yes
mol_id organism_scientific organism_common expression_system
4 Homo sapiens Human Escherichia coli
gene: POLB
Authors : Batra, V.K., Beard, W.A., Shock, D.D., Pedersen, L.C., Wilson, S.H.
Keywords : Nucleotidyl Transferase, DNA Polymerase, Misincorporation, DNA damage, DNA repair, DNA replication, DNA synthesis, DNA-binding, DNA-directed DNA polymerase, Lyase, Magnesium, Metal-binding, Nucleotidyltransferase, Nucleus, Polymorphism, Sodium, TRANSFERASE-DNA COMPLEX
Exp. method : X-RAY DIFFRACTION ( 2.60 Å )
Citation :

Structures of DNA polymerase beta with active-site mismatches suggest a transient abasic site intermediate during misincorporation.

Batra, V.K.,Beard, W.A.,Shock, D.D.  et al.
(2008)  Mol.Cell  30 : 315 - 324

PubMed: 18471977
DOI: 10.1016/j.molcel.2008.02.025

Reaction

Chain : A
UniProt : P06746 (DPOLB_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 -
-
a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)- 4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-phospho-2'- deoxyribonucleoside-DNA + H(+) - PubMed:9572863, PubMed:9614142
-
2'-deoxyribonucleotide-(2'-deoxyribose 5'-phosphate)-2'- deoxyribonucleotide-DNA = a 3'-end 2'-deoxyribonucleotide-(2,3- dehydro-2,3-deoxyribose 5'-phosphate)-DNA + a 5'-end 5'-phospho-2'- deoxyribonucleoside-DNA + H(+) 4.2.99.18 PubMed:9614142
-
Cofactor: Evidence: Note:
Mg(2+) ECO:0000269 | PubMed:9287163
Binds 2 magnesium ions per subunit.