Brand  (β version)

PDB ID: 6CTR

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Ligands
Code Name Style Show Link
CL Chloride ion PoSSuM
DC 2'-deoxycytidine-5'-monophosphate PoSSuM
F3C 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine PoSSuM
FF4 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]cytidine PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
2DA 2',3'-dideoxyadenosine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6CTR   PDBj   RCSB PDB   PDBe
Header : transcription/dna
Title : Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF (R & S isomers), beta, gamma dCTP analogue
Release Data : 2018-06-20
Compound :
mol_id molecule chains
1 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
2 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(2DA))-3') P
mol_id molecule chains
3 DNA (5'-D(P*GP*TP*CP*GP*G)-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 Homo sapiens  (taxid:9606)
synthetic: yes
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 organism_common expression_system
4 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: POLB
expression_system_strain: Tap56
expression_system_vector_type: Plasmid
expression_system_plasmid: pwl-11
Authors : Batra, V.K., Wilson, S.H.
Keywords : DNA Polymerase Beta, Conformational Change, enzyme mechanism, LFER, transcription-dna complex
Exp. method : X-RAY DIFFRACTION ( 1.85 Å )
Citation :

Mapping Functional Substrate-Enzyme Interactions in the pol beta Active Site through Chemical Biology: Structural Responses to Acidity Modification of Incoming dNTPs.

Batra, V.K.,Oertell, K.,Beard, W.A.  et al.
(2018)  Biochemistry  57 : 3934 - 3944

PubMed: 29874056
DOI: 10.1021/acs.biochem.8b00418

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.