Structure of PDB 8jch Chain M Binding Site BS02

Receptor Information
>8jch Chain M (length=721) Species: 559292 (Saccharomyces cerevisiae S288C) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPSFFRWLSRKYPKIISPVLEEQPQIVDGVILPLDYSASNPNGELDNLYL
DMNGIVHPCSHPENKPPPETEDEMLLAVFEYTNRVLNMARPRKVLVMAVD
GVAPRAKMNQQRARRFRSARDAQIENEAREEIMRQRDAVRNKKTWDSNAI
TPGTPFMDKLAAALRYWTAFKLATDPGWKNLQVIISDATVPGEGEHKIMN
FIRSQRADPEYNPNTTHCIYGLDADLIFLGLATHEPHFKILREDVFAQDN
RKREEEKQFLQKQNSEQPFLWLHINVLREYLSAELWVPGLPFTFDLERAI
DDWVFMCFFCGNDFLPHLPCLDVRENSIDILLDIWKVVLPKLKTYMTCDG
VLNLPSVETLLQHLGSREGDIFKTRHIQEARKKEEFVKLFEPGYHERYYT
AKFHVTPQDIEQLRKDMVKCYIEGVAWVLMYYYQGCASWNWFYPYHYAPL
ATDFHGFSHLEIKFEEGTPFLPYEQLMSVLPAASGHALPKIFRSLMSEPD
SEIIDFYPEEFPIDMNGKKMSWQGIALLPFIDQDRLLTAVRAQYPLLSDA
ERARNIRGEPVLLISNKNANYERFSKKLYSKENNNNNVVVKFQHFKSGLS
GIVSKDVEGFELNGKIVCPIQGGSLPNLSTTLILKMSYRLIPLPSRNKSI
ILNGFIPSEPVLTAYDLDSIMYKYNNQNYSRRWNFGNDLKQNIVPVGPKG
ITQYKPRTGGYRAFFYFAELS
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 chain8jch Chain M Residue 2001 [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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PDB8jch Structural basis of exoribonuclease-mediated mRNA transcription termination
Resolution2.7 Å
Binding residue
(original residue number in PDB)		D233 D333
Binding residue
(residue number reindexed from 1)		D223 D313
Annotation score4
Enzymatic activity
Enzyme Commision number 3.1.13.-
Gene Ontology
Molecular Function
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003729 mRNA binding
GO:0004527 exonuclease activity
GO:0004534 5'-3' RNA exonuclease activity
GO:0005515 protein binding
GO:0019843 rRNA binding
Biological Process
GO:0000398 mRNA splicing, via spliceosome
GO:0000448 cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006139 nucleobase-containing compound metabolic process
GO:0006353 DNA-templated transcription termination
GO:0006364 rRNA processing
GO:0006397 mRNA processing
GO:0030846 termination of RNA polymerase II transcription, poly(A)-coupled
GO:0030847 termination of RNA polymerase II transcription, exosome-dependent
GO:0034244 negative regulation of transcription elongation by RNA polymerase II
GO:0043144 sno(s)RNA processing
GO:0071028 nuclear mRNA surveillance
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
GO:0110155 NAD-cap decapping
GO:1904595 positive regulation of termination of RNA polymerase II transcription
Cellular Component
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0090730 Las1 complex
GO:0110103 RNA polymerase II termination complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:8jch, PDBe:8jch, PDBj:8jch
PDBsum8jch
PubMed38538796
UniProtQ02792|XRN2_YEAST 5'-3' exoribonuclease 2 (Gene Name=RAT1)

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