Structure of PDB 8ppv Chain A Binding Site BS02

Receptor Information
>8ppv Chain A (length=447) Species: 272844 (Pyrococcus abyssi GE5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EYSKYEDVVIEWNPSVTPVQIEKNYEVKFDVRQVKLRPPKVKNGSGKEGE
IIVEAYASLFKSRLSKLKRILRENPEISNVVDIGKLNYVSGDEEVTIIGL
VNSKRETNRGLIFEVEDKTGIVKVFLPKDSEDYREAFKVLPDAVVAFKGF
YSKKGIFFANKFYLPDVPLYRKQKPPLEEKVYAILISDIHVGSREFCEKA
FLKFLEWLNGHVESKEEEEIVSRVKYLIIAGDVVDGIGIYPGQYSDLVIP
DIFDQYEALANLLANVPEHITMFIGPGNADAARPAIPQPEFYKEYAKPIY
KLKNAIIISNPAVIRLHGRDFLIAHGRGIEDVVSFVPGLTHHKPGLPMVE
LLKMRHLAPTFGGKVPIAPDPEDLLVIEEVPDLVQMGHVHVYDAVVYRGV
QLVNSATWQAQTEFQKMVNIVPTPAKVPVVDVESARVVKVLDFSGWC
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 chain8ppv Chain A Residue 701 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8ppv Molecular basis for proof-reading by Family-D DNA polymerases
Resolution3.02 Å
Binding residue
(original residue number in PDB)		D360 D404 H562
Binding residue
(residue number reindexed from 1)		D188 D232 H390
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:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003887 DNA-directed DNA polymerase activity
GO:0004527 exonuclease activity
GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
GO:0008408 3'-5' exonuclease activity
Biological Process
GO:0006260 DNA replication
GO:0006261 DNA-templated DNA replication
GO:0006271 DNA strand elongation involved in DNA replication
GO:0006308 DNA catabolic process
GO:0071897 DNA biosynthetic process
Cellular Component
GO:0042575 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:8ppv, PDBe:8ppv, PDBj:8ppv
PDBsum8ppv
PubMed38097591
UniProtQ9V2F3|DP2S_PYRAB DNA polymerase II small subunit (Gene Name=polB)

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