Structure of PDB 8b76 Chain A Binding Site BS04

Receptor Information
>8b76 Chain A (length=1118) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVG
WLTNMHATLVSQNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESR
VNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQ
LFEARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVSI
DKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAV
DQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDE
VALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFA
PDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELD
PELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPD
ETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVG
GHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVD
KVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQ
PDSIKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKK
KVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENP
FYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDS
LQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERV
GRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKF
TNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKR
YAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSA
VASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSIT
TARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPI
KRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVS
NPVPRVEHPDWLKRKIAT
Ligand information
Ligand IDCA
InChIInChI=1S/Ca/q+2
InChIKeyBHPQYMZQTOCNFJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Ca++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Ca+2]
FormulaCa
NameCALCIUM ION
ChEMBL
DrugBankDB14577
ZINC
PDB chain8b76 Chain A Residue 1203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB8b76 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		D640 V641 D877
Binding residue
(residue number reindexed from 1)		D585 V586 D809
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.-
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication
GO:0006281 DNA repair
Cellular Component
GO:0008622 epsilon DNA polymerase complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8b76, PDBe:8b76, PDBj:8b76
PDBsum8b76
PubMed37819038
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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