Brand  (β version)

PDB ID: 5BPC

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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
Code Name Show
4U3 5-chloro-2'-deoxycytidine 5'-(dihydrogen phosphate)
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5BPC   PDBj   RCSB PDB   PDBe
Header : Transferase, ligase/DNA
Title : DNA polymerase beta ternary complex with a templating 5ClC and incoming dATP analog
Release Data : 2015-08-19
Compound :
mol_id molecule chains
1 DNA polymerase beta A
ec: 2.7.7.7,4.2.99.-
mol_id molecule chains
2 DNA (5'-D(P*GP*TP*CP*GP*G)-3') D
mol_id molecule chains
3 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*C)-3') P
mol_id molecule chains
4 DNA (5'-D(*CP*CP*GP*AP*CP*(CDO)P*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: POLB
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
4 Synthetic construct  (taxid:32630)
synthetic: yes
Authors : Freudenthal, B.D., Wilson, S.H.
Keywords : TRANSFERASE, LYASE/DNA, ligase-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.0 Å )
Citation :

Intrinsic mutagenic properties of 5-chlorocytosine: A mechanistic connection between chronic inflammation and cancer.

Fedeles, B.I.,Freudenthal, B.D.,Yau, E.  et al.
(2015)  Proc.Natl.Acad.Sci.USA  112 : E4571 - E4580

PubMed: 26243878
DOI: 10.1073/pnas.1507709112

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.