Structure of PDB 7opk Chain A Binding Site BS02

Receptor Information

>7opk Chain A (length=649) Species: 759272 (Thermochaetoides thermophila DSM 1495)

GIPAAFRWLSNKYPKIISPVVEERPIVMPDGTEIPVDATRPNPNGEEFDN
LYLDMNGIVHPCSHPEDKPAPKDEEEMMIEIFKYTDRIVKMVRPRKILMI
AVDGVAPRAKMNQQRSRRFRAAQEAKEKEEEKKKAFDSNSITPGTPFMDI
LAASLRYWCAYKLNTDPAWAKLKVIISDATVPGEGEHKIMEFIRSQRSSP
EHNPNTRHVIYGLDADLIMLGLATHEPHFRVLREDVFFQEKPFIWLHVSI
LREYLAAELEVPNLPFRWDLERAIDDWVFLCFFVGNDFLPHLPALEIREN
GIDTLTAIWKDNLPIMGGYLTKDGHVDLERAQYILNGLAKQEDAIFRRRR
EVEERREAVDTVRLWEEGYADRYYEQKFKVDPKDIEFRHKVGRAYAEGLA
WVLQYYYQGCPSWEWFYPYHYAPFAADFVDLAKMEIKFEKGRISRPFEQL
MSVLPAASRHAIPEVYHDLMTDPNSPIIDFYPEEFEIDLNGKKMAWQGVA
LLPFIEMPRLLAAMKEREHLLSEEDRARNEPGFDVLLISDAHPGLYEDIT
SHFYSKKQGAPKFKLNPRRSDGLAGKVEKIEGYVPHGSLVYPLARNSMPD
VDYDRSITVRYIMPSSAHQHKSMLLRGVKLPPPALSRSDIEIIRSKAKN

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 7opk Chain A Residue 902

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7opk Observation of conformational changes that underlie the catalytic cycle of Xrn2.
• Resolution: 3.0 Å
• Binding residue (original residue number in PDB): E211 D239 D241
• Binding residue (residue number reindexed from 1): E186 D214 D216
• Annotation score: 4

Enzymatic activity

• Enzyme Commision number: 3.1.13.-

Gene Ontology

Molecular Function

• GO:0003676 nucleic acid binding
• GO:0004527 exonuclease activity
• GO:0004534 5'-3' RNA exonuclease activity

Biological Process

• GO:0006139 nucleobase-containing compound metabolic process

Cellular Component

• GO:0005634 nucleus

External links

• PDB: RCSB:7opk, PDBe:7opk, PDBj:7opk
• PDBsum: 7opk
• PubMed: 36008487
• UniProt: G0S058