Brand  (β version)

PDB ID: 3TFR

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
CL Chloride ion PoSSuM
F3A 2'-deoxy-5'-O-[(S)-{difluoro[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}(hydroxy)phosphoryl]adenosine PoSSuM
MG Magnesium ion PoSSuM
NA Sodium ion PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 3TFR   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Ternary complex structure of DNA polymerase beta with a gapped DNA substrate and a, B dAMP(CF2)PP in the active site
Release Data : 2012-03-21
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*TP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') T
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(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
expression_system_strain: Tap56
expression_system_vector_type: plasmid
expression_system_plasmid: pWL11
mol_id organism_scientific
2
synthetic: yes
mol_id organism_scientific
3
synthetic: yes
mol_id organism_scientific
4
synthetic: yes
Authors : Chamberlain, B.T., Batra, V.K., Beard, W.A., Kadina, A.P., Shock, D.D., Kashemirov, B.A., McKenna, C.E., Goodman, M.F., Wilson, S.H.
Keywords : DNA Polymerase, stereoselectivity, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.000 Å )
Citation :

Stereospecific Formation of a Ternary Complex of (S)-alpha, beta-Fluoromethylene-dATP with DNA Pol beta.

Chamberlain, B.T.,Batra, V.K.,Beard, W.A.  et al.
(2012)  Chembiochem  13 : 528 - 530

PubMed: 22315190
DOI: 10.1002/cbic.201100738

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 -
-
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
-
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
-