Structure of PDB 5j8n Chain A Binding Site BS01

Receptor Information

>5j8n Chain A (length=258) Species: 192952 (Methanosarcina mazei Go1)

AEHYNLISWNVNGLRAAVKKGFLDLLLEHRFDIVCVQETKVSQDKLPREV
KNIQGYYNYFVSAEQNGYSGVGTFSKNKPIKLEKGMGIEVFDREGRFLRT
DYEDFVLLNIYFPNGKMSQERLGYKMAFYDAFLDYANALKSEGKKLVICG
DVNTAHKEIDLARPKQNEMISGFLPEERAWMDKFLAAGYLDSFRMFNPEG
GNYSWWSYRTGARSRNVGWRLDYVFVSENLRENVKSASIYPEIMGSDHCP
VGLELEFV

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: 5j8n Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5j8n Structure of the archael ExoIII homologue Mm3148 at 1.4 Angstrom
• Resolution: 1.44 Å
• Binding residue (original residue number in PDB): N13 E39
• Binding residue (residue number reindexed from 1): N12 E38
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N11 N13 E39 Y112 D152 N154 D223 D248 H249
• Catalytic site (residue number reindexed from 1): N10 N12 E38 Y111 D151 N153 D222 D247 H248
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008311 double-stranded DNA 3'-5' DNA exonuclease activity
• GO:0016787 hydrolase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006281 DNA repair
• GO:0006284 base-excision repair

External links

• PDB: RCSB:5j8n, PDBe:5j8n, PDBj:5j8n
• PDBsum: 5j8n
• UniProt: Q8PSD1