Brand  (β version)

PDB ID: 4RT3

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Ligands
Code Name Style Show Link
C6T 2'-deoxy-5'-O-[(S)-hydroxy{[(R)-hydroxy(phosphonomethyl)phosphoryl]amino}phosphoryl]-3,4-dihydrothymidine PoSSuM
CL Chloride ion PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
DOC 2',3'-dideoxycytidine-5'-monophosphate
Glycosylation
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Modification
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Structure summary

Code : 4RT3   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Ternary complex crystal structure of DNA polymerase Beta with (alpha, beta)-NH-(beta,gamma)-CH2-dTTP
Release Data : 2015-07-01
Compound :
mol_id molecule chains
1 DNA polymerase beta A
ec: 2.7.7.7, 4.2.99.-
mol_id molecule chains synonym
2 DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T Template Strand
mol_id molecule chains synonym
3 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(DOC))-3') P Primer Strand
mol_id molecule chains synonym
4 DNA (5'-D(P*GP*TP*CP*GP*G)-3') D Downstream Primer Strand
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: POLB
expression_system_vector_type: Plasmid
expression_system_plasmid: pWL11
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 : Batra, V.K., Wilson, S.H.
Keywords : DNA Polymerase Beta, Ternary complex, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 1.92 Å )
Citation :

Two Scaffolds from Two Flips: (alpha, beta)/(beta, gamma) CH2/NH "Met-Im" Analogues of dTTP.

Kadina, A.P.,Kashemirov, B.A.,Oertell, K.  et al.
(2015)  Org.Lett.  17 : 2586 - 2589

PubMed: 25970636
DOI: 10.1021/acs.orglett.5b00799

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.