Structure of PDB 8ppu Chain B Binding Site BS06

Receptor Information
>8ppu Chain B (length=1191) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ELPKEMEEYFEMLQREIDKAYEIAKKARAQGKDPSLDVEIPQATDMAGRV
ESLVGPPGVAKRIRELVKEYGKEIAALKIVDEIIEGKFGDLGSREKYAEQ
AVRTALAILTEGIVSAPIEGIANVKIKRNTWADNSEYLALYYAGPIRSSG
GTAQALSVLVGDYVRRKLGLDRFKPSEKHIERMVEEVDLYHRAVTRLQYH
PSPEEVRLAMRNIPIEITGEATDDVEVSHRDVPGVETNQLRGGAILVLAE
GVLQKAKKLVKYIDKMGIEGWEWLKEFVEAKEVDMGFYYSLYQKFKEEIA
PSDKYAKEVIGGRPLFSDPSKPGGFRLRYGRSRASGFATWGINPATMILV
DEFLAIGTQLKTERPGKGAVVTPVTTIEGPIVKLKDGSVLRVDDYNLALK
VREDVEEILYLGDAVIAFGDFVENNQTLLPANYCEEWWILEFVKALKEIY
EVHLEPFTENEEESIEEASDYLEIDPEFLKEMLRDPLRVKPPVELAIHFS
EVLGIPLHPYYTLYWNSVEPKDVEKLWRLLKNYAEIEWSNFRGIKFAKKI
VISQEKLGDSKRTLELLGLPHTVRDGNVIVDYPWAAALLTPLGNLNWEFM
AKPLYATIDIINENNEIKLRDRGISWIGARMGRPEKAKERKMKPPVQVLF
PIGLAGGSSRDIKKAAEEGKVAEVEIAFFKCPKCGHVGPEHLCPNCGTRK
ELLWVCPRCNAEYPESQAEGYNYTCPKCNVKLRPYAKRKIRPSELLNRAM
ENVKVYGVDKLKGVMGMTSGWKMPEPLEKGLLRAKNDVYVFKDGTIRFDA
TDAPITHFRPREIGVSVEKLRELGYTHDFEGKPLVSEDQIVELKPQDIIL
SKEAGRYLLKVAKFVDDLLEKFYGLPRFYNAEKMEDLIGHLVIGLAPHTS
AGIVGRIIGFVDALVGYAHPYFHAAKRRNCDGDEDAVMLLLDALLNFSRY
YLPEKRGGKMDAPLVITTRLDPREVDSEVHNMDIVRYYPLEFYEATYELK
SPKELVGVIERVEDRLGKPEMYYGLKFTHDTDDIALGPKMSLYKQLGDME
EKVRRQLEVAKRIRAVDEHGVAEKILNSHLIPDLRGNLRSFTRQEFRCVK
CNTKFRRPPLNGKCPVCGGKIVLTVSKGAIEKYLGTAKMLVTEYNVKNYT
RQRICLTERDIDSLFENVFPETQLTLIVNPNDICQRLVMAR
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 chain8ppu Chain B Residue 1304 [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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PDB8ppu Molecular basis for proof-reading by Family-D DNA polymerases
Resolution3.02 Å
Binding residue
(original residue number in PDB)		N954 D956 D958
Binding residue
(residue number reindexed from 1)		N929 D931 D933
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.7: DNA-directed DNA polymerase.
3.1.11.1: exodeoxyribonuclease I.
Gene Ontology
Molecular Function
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
Biological Process
GO:0006260 DNA replication

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Molecular Function
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Biological Process
External links
PDB RCSB:8ppu, PDBe:8ppu, PDBj:8ppu
PDBsum8ppu
PubMed38097591
UniProtQ9V2F4|DP2L_PYRAB DNA polymerase II large subunit (Gene Name=polC)

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