Brand  (β version)

PDB ID: 6CR5

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Ligands
Code Name Style Show Link
FCJ 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]oxy}phosphoryl]adenosine PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
DOC 2',3'-dideoxycytidine-5'-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6CR5   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CH2-beta, gamma dATP analogue
Release Data : 2018-07-18
Compound :
mol_id molecule chains
1 Template Strand T
mol_id molecule chains
2 Primer Strand P
mol_id molecule chains
3 Downstream Primer Strand D
mol_id molecule chains
4 DNA polymerase beta A
ec: 2.7.7.7,4.2.99.-
Source :
mol_id organism_scientific organism_common
1 Homo sapiens  (taxid:9606) Human
synthetic: yes
mol_id organism_scientific organism_common
2 Homo sapiens  (taxid:9606) Human
synthetic: yes
mol_id organism_scientific organism_common
3 Homo sapiens  (taxid:9606) Human
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 : Conformational Change, enzyme mechanism, LFER, Acidity modification, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 1.9820 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:
a 2'-deoxyribonucleoside 5'-triphosphate + DNA(n) = diphosphate + DNA(n+1) 2.7.7.7 -
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a 5'-end 2'-deoxyribose-2'-deoxyribonucleotide-DNA = (2E,4S)- 4-hydroxypenten-2-al-5-phosphate + a 5'-end 5'-monophospho-2'- deoxyribonucleoside-DNA + H(+) - PubMed:9572863, PubMed:9614142
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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'-monophospho- 2'-deoxyribonucleoside-DNA + H(+) 4.2.99.18 PubMed:9614142
-