Structure of PDB 8d9d Chain C Binding Site BS03

Receptor Information
>8d9d Chain C (length=1058) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQVFHFYWLDAYEDQYNQPGVVFLFGKVWIESAETHVSCCVMVKNIERTL
YFLPREMKIDLNTGKETGTPISMKDVYEEFDEKIATKYKIMKFKSKPVEK
NYAFEIPDVPEKSEYLEVKYSAEMPQLPQDLKGETFSHVFGTNTSSLELF
LMNRKIKGPCWLEVKSPQLLNQPVSWCKVEAMALKPDLVNVIKDVSPPPL
VVMAFSMKTMQNAKNHQNEIIAMAALVHHSFALDKAAPKPPFQSHFCVVS
KPKDCIFPYAFKEVIEKKNVKVEVAATERTLLGFFLAKVHKIDPDIIVGH
NIYGFELEVLLQRINVCKAPHWSKIGRLKRSNMPKLGFGERNATCGRMIC
DVEISAKELIRCKSYHLSELVQQILKTERVVIPMENIQNMYSESSQLLYL
LEHTWKDAKFILQIMCELNVLPLALQITNIAGNIMSRTLMGGRSERNEFL
LLHAFYENNYIVPDKQIAAYAGGLVLDPKVGFYDKFILLLDFNSLYPSII
QEFNICFTTVQRVEQIPELPDPSLEMGILPREIRKLVERRKQVKQLMKQQ
DLNPDLILQYDIRQKALKLTANSMYGCLGFSYSRFYAKPLAALVTYKGRE
ILMHTKEMVQKMNLEVIYGDTDSIMINTNSTNLEEVFKLGNKVKSEVNKL
YKLLEIDIDGVFKSLLLLKKKKYAALVVEPTSDGNYVTKQELKGLDIVRR
DWCDLAKDTGNFVIGQILSDQSRDTIVENIQKRLIEIGENVLNGSVPVSQ
FEINKALTKDPQDYPDKKSLPHVHVALWINSQGGRKVKAGDTVSYVICQD
GSNLTASQRAYAPEQLQKQDNLTIDTQYYLAQQIHPVVARICEPIDGIDA
VLIATWLGLDPTQFRVHHYTDEEKYRDCERFKCPCPTCGTENIYDNVFDG
SGTDMEPSLYRCSNIDCKASPLTFTVQLSNKLIMDIRRFIKKYYDGWLIC
EEPTCRNRTRHLPLQFSRTGPLCPACMKATLQPEYSDKSLYTQLCFYRYI
FDAECALEKLTTDHEKDKLKKQFFTPKVLQDYRKLKNTAEQFLSRSGYSE
VNLSKLFA
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain8d9d Chain C Residue 1501 [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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PDB8d9d Structures of human primosome elongation complexes.
Resolution3.59 Å
Binding residue
(original residue number in PDB)		D860 F861 D1004
Binding residue
(residue number reindexed from 1)		D491 F492 D622
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003688 DNA replication origin binding
GO:0003697 single-stranded DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0019901 protein kinase binding
GO:0046872 metal ion binding
Biological Process
GO:0000731 DNA synthesis involved in DNA repair
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006269 DNA replication, synthesis of primer
GO:0006270 DNA replication initiation
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006272 leading strand elongation
GO:0006273 lagging strand elongation
GO:0006281 DNA repair
GO:0006289 nucleotide-excision repair
GO:0006303 double-strand break repair via nonhomologous end joining
GO:0032479 regulation of type I interferon production
GO:1902975 mitotic DNA replication initiation
GO:1904161 DNA synthesis involved in UV-damage excision repair
Cellular Component
GO:0000785 chromatin
GO:0005634 nucleus
GO:0005635 nuclear envelope
GO:0005654 nucleoplasm
GO:0005658 alpha DNA polymerase:primase complex
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016363 nuclear matrix
GO:0031981 nuclear lumen

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8d9d, PDBe:8d9d, PDBj:8d9d
PDBsum8d9d
PubMed37069376
UniProtP09884|DPOLA_HUMAN DNA polymerase alpha catalytic subunit (Gene Name=POLA1)

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