Structure of PDB 8df9 Chain B Binding Site BS05

Receptor Information

>8df9 Chain B (length=845) Species: 2320 (Methanopyrus kandleri)

ALVYDAEFVGSEREFEEERETFLKGVKAYDGVLATRYLMERSSSAKNDEE
LLELHQNFILLTGSYACSIDPTEDRYQNVIVRGVNFDERVQRLSTGGSPA
RYAIVYRRGWRAIAKALDIDEEDVPAIEVRAVKRNPLQPALYRILVRYGR
VDLMPVTVDEVPPEMAGEFERLIERYDVPIDEKEERILEILRENPWTPHD
EIARRLGLSVSEVEGEKDPESSGIYSLWSRVVVNIEYDERTAKRHVKRRD
RLLEELYEHLEELSERYLRHPLTRRWIVEHKRDIMRRYLEQRIVECALKL
QDRYGIREDVALCLARAFDGSISMIATTPYRTLKDVCPDLTLEEAKSVNR
TLATLIDEHGLSPDAADELIEHFESIAGILATDLEEIERMYEEGRLSEEA
YRAAVEIQLAELTKKEGVGRKTAERLLRAFGNPERVKQLAREFEIEKLAS
VEGVGERVLRSLVPGYASLISIRGIDRERAERLLKKYGGYSKVREAGVEE
LREDGLTDAQIRELKGLKTLESIVGDLEKADELKRKYGSASAVRRLPVEE
LRELGFSDDEIAEIKGIPKKLREAFDLETAAELYERYGSLKEIGRRLSYD
DLLELGATPKAAAEIKGPEFKFLLNIEGVGPKLAERILEAVDYDLERLAS
LNPEELAEKVEGLGEELAERVVYAARERVESRRKSGRQERSEEEWKEWLE
RKVGEGRARRLIEYFGSAGEVGKLVENAEVSKLLEVPGIGDEAVARLVPG
YKTLRDAGLTPAEAERVLKRYGSVSKVQEGATPDELRELGLGDAKIARIL
GLRSLVNARLDVDTAYELARRYGSVSAAELRELGLSDRAIARIAG

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: 8df9 Chain B Residue 901

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8df9 Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism.
• Resolution: 3.24 Å
• Binding residue (original residue number in PDB): I471 I473 I476
• Binding residue (residue number reindexed from 1): I470 I472 I475
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0003677 DNA binding

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:8df9, PDBe:8df9, PDBj:8df9
• PDBsum: 8df9
• PubMed: 35969036
• UniProt: Q977W1