Brand  (β version)

PDB ID: 5DB6

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Ligands
Code Name Style Show Link
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
FMG 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7-methyl-6-oxo-6,9-dihydro-1h-purin-7-ium
Glycosylation
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Structure summary

Code : 5DB6   PDBj   RCSB PDB   PDBe
Header : transferase/dna
Title : Structure of human DNA polymerase beta Host-Guest complex with the N7MG base paired with a dC
Release Data : 2015-11-11
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(*CP*CP*GP*AP*CP*GP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T
mol_id molecule chains
3 DNA (5'-D(*GP*CP*TP*(FMG)P*AP*TP*GP*CP*GP*A)-3') P
mol_id molecule chains
4 DNA (5'-D(P*GP*TP*CP*GP*G)-3') D
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 Homo sapiens  (taxid:9606)
synthetic: yes
mol_id organism_scientific
3 Homo sapiens  (taxid:9606)
synthetic: yes
mol_id organism_scientific
4 Homo sapiens  (taxid:9606)
synthetic: yes
Authors : Koag, M.C., Lee, S.
Keywords : human DNA polymerase, transferase-dna complex
Exp. method : X-RAY DIFFRACTION ( 2.83 Å )
Citation :

N7 Methylation Alters Hydrogen-Bonding Patterns of Guanine in Duplex DNA.

Kou, Y.,Koag, M.C.,Lee, S.
(2015)  J.Am.Chem.Soc.  137 : 14067 - 14070

PubMed: 26517568
DOI: 10.1021/jacs.5b10172

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.