Brand  (β version)

PDB ID: 4DOA

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
FHG 2'-deoxy-5'-O-[(R)-{[(R)-[(S)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine 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 : 4DOA   PDBj   RCSB PDB   PDBe
Header : TRANSFERASE/DNA
Title : Ternary complex of DNA polymerase beta with a dideoxy terminated primer and 2'-deoxyguanosine 5'-beta, gamma-monofluoromethylene triphosphate: non-interactive binding of S-isomer
Release Data : 2012-06-13
Compound :
mol_id molecule chains
1 DNA polymerase beta A
ec: 2.7.7.7, 4.2.99.-
fragment: DNA Polymerase Beta
mol_id molecule chains
2 C C G A C C G C G C A T C A G C T
mol_id molecule chains
3 G C T G A T G C G (DOC) P
mol_id molecule chains
4 G T C G G 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
other_details: Chemically synthesized oligonucleotide
mol_id organism_scientific
3
synthetic: yes
other_details: Chemically synthesized oligonucleotide
mol_id organism_scientific
4
synthetic: yes
other_details: Chemically synthesized oligonucleotide
Authors : Batra, V.K.
Keywords : Stereoselectivity, polymerase, DNA Polymerase, TRANSFERASE-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.051 Å )
Citation :

Beta,gamma-CHF- and beta,gamma-CHCl-dGTP Diastereomers: Synthesis, Discrete (31)P NMR Signatures, and Absolute Configurations of New Stereochemical Probes for DNA Polymerases

Wu, Y.,Zakharova, V.M.,Kashemirov, B.A.  et al.
(2012)  J.Am.Chem.Soc.  134 : 8734 - 8737

PubMed: 22397499
DOI: 10.1021/ja300218x

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.