Structure of PDB 8kg6 Chain M Binding Site BS02

Receptor Information
>8kg6 Chain M (length=813) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YANSTWEVLQYKDSGEPGVLEVFVTINGKVQNITFHIPKTIYMKFKSQTM
PLQKIKNCLIEKSSASLPNTLPESVFLEEKENCTSIFNDENVLGVFEGTI
TPHQRAIMDLGASVTFRSKAMGALGKGIQQGFEMKDLSMAENERYLSGFS
MDIGYLLHFPTSIGYEFFSLFKSWGDTITINASSLGQIYKQMFEKKKGKI
ETYSYLVDIKEDINFEFVYFTDISKLYRRLSQETTKLKEERGLQFLLLLQ
SPFITKLLGTIRLLNQMPIVKLSLQPTLLKKLVNHVLSSGSWISHLIKLS
QYSNIPICNLRLDSMDYIIDVLYARKLKKENIVLWWNEKAPLPDHGGIQN
DFDLNTSWIMNDSEFPKINNSGVYDNVVLDVGVDNLTVNTILTSALFVHD
AFSNDALNVLRGMLKEWWDEALKENSTADLLVNSLASWVQNPNAKLFDGL
LRYHVHNLTKKALLQLVNEFSALGSTIVYADRNQILIKTNKYSPENCYAY
SQYMMKAVRTNPMFSYLDLNIKRYWDLLIWMDKFNFSGLACDYTAVSQWQ
LKKFLSPIYQPEFEDWMMIILDSMLKTKQSYLKLNSSVENSLNGFSHLFS
KPLMKRVKKLFKNQQEFILDPQYEADYVIPVLPGSHLNVKNPLLELVKSL
CHVMLLSKSTILEIRTLRKELLKIFELREFAKVAEFKDPSLSLVVPDFLC
EYCFFISDIDFCKAAPESIFSCVRCHKAFNQVLLQEHLIQKLRSDIESYL
IQDLRCSRCHKVKRDYMSAHCPCAGAWEGTLPRESIVQKLNVFKQVAKYY
GFDILLSCIADLT
Ligand information
Ligand IDZN
InChIInChI=1S/Zn/q+2
InChIKeyPTFCDOFLOPIGGS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341[Zn++]
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Zn+2]
FormulaZn
NameZINC ION
ChEMBLCHEMBL1236970
DrugBankDB14532
ZINC
PDB chain8kg6 Chain M Residue 3002 [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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PDB8kg6 Synergism between CMG helicase and leading strand DNA polymerase at replication fork.
Resolution3.07 Å
Binding residue
(original residue number in PDB)		C2164 C2167 C2179
Binding residue
(residue number reindexed from 1)		C756 C759 C771
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:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0003729 mRNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
GO:0016787 hydrolase activity
GO:0032183 SUMO binding
GO:0046872 metal ion binding
GO:0051539 4 iron, 4 sulfur cluster binding
Biological Process
GO:0000278 mitotic cell cycle
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006272 leading strand elongation
GO:0006281 DNA repair
GO:0006284 base-excision repair
GO:0006287 base-excision repair, gap-filling
GO:0006297 nucleotide-excision repair, DNA gap filling
GO:0006302 double-strand break repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0007064 mitotic sister chromatid cohesion
GO:0031573 mitotic intra-S DNA damage checkpoint signaling
GO:0033314 mitotic DNA replication checkpoint signaling
GO:0035822 gene conversion
GO:0042276 error-prone translesion synthesis
GO:0045004 DNA replication proofreading
Cellular Component
GO:0005634 nucleus
GO:0005657 replication fork
GO:0008622 epsilon DNA polymerase complex
GO:0043231 intracellular membrane-bounded organelle
GO:0043596 nuclear replication fork

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8kg6, PDBe:8kg6, PDBj:8kg6
PDBsum8kg6
PubMed37730685
UniProtP21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)

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