Structure of PDB 5yjj Chain C Binding Site BS02

Receptor Information
>5yjj Chain C (length=442) Species: 176280 (Staphylococcus epidermidis ATCC 12228) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KKVFKTEWAGRSLTIETGQLAKQANGAVLVRYGDTVVLSTATASKEPRFF
PLTVNYEEKMYAADEATLTARLIDRPIRPLFPKGYRHDVQIMNIVLSADP
DCSPEMAAMIGSSMALSVSDIPFQGPIAGVNVGYIDGKYVINPSVADKEI
SRLDLEVAGHKDAVNMVEAGASEITESEMLEAIFFGHEEIKRLVAFQQEI
IDHIQPIKQVYAILNDLIKEEVRRLIADEKIRPDGRKVDEIRPLESEVGL
LPRAHGSGLFTRGQTQALSVLTLGARFMHHYNFPNFSVGETGPVRAPGRR
EIGHGALGERALRYIIPDTQDFPYTIRIVSEVLESNGSSSQASICGSTLA
LMDAGVPIKAPVAGIAMGLVTRDDSYTILTDIQGMEDALGDMDFKVAGTK
DGITAIQMDIKIDGLTREVIEEALEQARQGRLAIMDHMLHTI
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 chain5yjj Chain C Residue 802 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5yjj Characterization of Staphylococcus epidermidis Polynucleotide phosphorylase and its interactions with ribonucleases RNase J1 and RNase J2.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		S441 I485 D496
Binding residue
(residue number reindexed from 1)		S338 I382 D393
Annotation score1
Enzymatic activity
Enzyme Commision number 2.7.7.8: polyribonucleotide nucleotidyltransferase.
Gene Ontology
Molecular Function
GO:0000175 3'-5'-RNA exonuclease activity
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004654 polyribonucleotide nucleotidyltransferase activity
GO:0016779 nucleotidyltransferase activity
GO:0046872 metal ion binding
Biological Process
GO:0006396 RNA processing
GO:0006401 RNA catabolic process
GO:0006402 mRNA catabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5yjj, PDBe:5yjj, PDBj:5yjj
PDBsum5yjj
PubMed29242153
UniProtQ8CST1|PNP_STAES Polyribonucleotide nucleotidyltransferase (Gene Name=pnp)

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