Brand  (β version)

PDB ID: 5KFQ

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
CA Calcium ion PoSSuM
DPO Diphosphate PoSSuM
GOL Glycerol PoSSuM
MN Manganese (II) ion PoSSuM
STP 2'-deoxyadenosine 5'-O-(1-thiotriphosphate) PoSSuM
Non-standard Residues
Code Name Show
AS 2-deoxy-adenosine -5'-thio-monophosphate
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 5KFQ   PDBj   RCSB PDB   PDBe
Header : replication, transferase/DNA
Title : Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 10 mM Mn2+ for 600s
Release Data : 2016-06-29
Compound :
mol_id molecule chains synonym
1 DNA polymerase eta A RAD30 homolog A,Xeroderma pigmentosum variant type protein
ec: 2.7.7.7
mol_id molecule chains
2 DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') T
mol_id molecule chains
3 DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*(AS))-3') P
Source :
mol_id organism_scientific organism_common expression_system
1 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:469008)
gene: POLH, RAD30, RAD30A, XPV
expression_system_strain: BL21(DE3)
expression_system_vector_type: plasmid
expression_system_plasmid: pET28
mol_id organism_scientific
2 Homo sapiens  (taxid:9606)
synthetic: yes
mol_id organism_scientific
3 Homo sapiens  (taxid:9606)
synthetic: yes
Authors : Gao, Y., Yang, W.
Keywords : in crystallo reaction, DNA polymerase, metal ion dependent catalysis, replication, transferase-DNA complex
Exp. method : X-RAY DIFFRACTION ( 1.5500 Å )
Citation :

Capture of a third Mg2+ is essential for catalyzing DNA synthesis.

Gao, Y.,Yang, W.
(2016)  Science  352 : 1334 - 1337

PubMed: 27284197
DOI: 10.1126/science.aad9633

Reaction

Chain : A
UniProt : Q9Y253 (POLH_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate 2.7.7.7 PubMed:27284197, PubMed:38212351
-
Cofactor: Evidence: Note:
Mn(2+) ECO:0000269 | PubMed:27284197
ECO:0000269 | PubMed:27284197
Binds 2 Mg(2+) (PubMed:27284197). Prefers Mg(2+), but can also use Mn(2+) (PubMed:27284197). In vitro, can also utilize other divalent cations such as Ca(2+) (PubMed:27284197).