Structure of PDB 8a5c Chain A Binding Site BS02

Receptor Information

>8a5c Chain A (length=237) Species: 243230 (Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539)

APLNAARPAEERAALLAWVKERLHEEYGDQDPTPRRDPMHELISTILSQR
TTHADEEAAYQELRTLGDWDAITLAPTDAVAHAIRRSNLPESKAPRIQET
LRRIKAAPGGYDLDFLRDLPVKDALKWLTDLPGVGVKTASLVLLFNYARP
VFPVDTHVHRVSTRVGVIPRMGEQAAHRALLALLPPDPPYLYELHINFLS
HGRQVCTWTRPKCGKCILRERCDAYALYGDKVPSFSE

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: 8a5c Chain A Residue 302

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8a5c Disentangling Unusual Catalytic Properties and the Role of the [4Fe-4S] Cluster of Three Endonuclease III from the Extremophile D. radiodurans.
• Resolution: 1.951 Å
• Binding residue (original residue number in PDB): I122 K123 A125 G127 G128
• Binding residue (residue number reindexed from 1): I104 K105 A107 G109 G110
• Annotation score: 4

Gene Ontology

Molecular Function

• GO:0000703 oxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
• GO:0003824 catalytic activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004519 endonuclease activity
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006285 base-excision repair, AP site formation
• GO:0006289 nucleotide-excision repair

External links

• PDB: RCSB:8a5c, PDBe:8a5c, PDBj:8a5c
• PDBsum: 8a5c
• PubMed: 35807515
• UniProt: Q9RRQ0