Structure of PDB 3aam Chain A Binding Site BS01

Receptor Information

>3aam Chain A (length=269) Species: 300852 (Thermus thermophilus HB8)

PRYGFHLSIAGKKGVAGAVEEATALGLTAFQIFAKSPRSWRPRALSPAEV
EAFRALREASGGLPAVIHASYLVNLGAEGELWEKSVASLADDLEKAALLG
VEYVVVHPGSGRPERVKEGALKALRLAGVRSRPVLLVENTAGGGEKVGAR
FEELAWLVADTPLQVCLDTCHAYAAGYDVAEDPLGVLDALDRAVGLERVP
VVHLNDSVGGLGSRVDHHAHLLQGKIGEGLKRVFLDPRLKDRVFILETPR
GPEEDAWNLRVFRAWLEEA

Ligand information

• Ligand ID: MN
• InChI: InChI=1S/Mn/q+2
• InChIKey: WAEMQWOKJMHJLA-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mn+2]
  CACTVS 3.341: [Mn++]
• Formula: Mn
• Name: MANGANESE (II) ION
• DrugBank: DB06757
• PDB chain: 3aam Chain A Residue 271

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3aam An additional C-terminal loop in endonuclease IV, an apurinic/apyrimidinic endonuclease, controls binding affinity to DNA
• Resolution: 1.58 Å
• Binding residue (original residue number in PDB): H172 D217 H219
• Binding residue (residue number reindexed from 1): H171 D216 H218
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): R39 H69 Y72 H108 E139 D169 H172 H204 D217 H219 E248
• Catalytic site (residue number reindexed from 1): R38 H68 Y71 H107 E138 D168 H171 H203 D216 H218 E247
• Enzyme Commision number: 3.1.21.2: deoxyribonuclease IV.

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003906 DNA-(apurinic or apyrimidinic site) endonuclease activity
• GO:0004519 endonuclease activity
• GO:0008081 phosphoric diester hydrolase activity
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding

Biological Process

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

External links

• PDB: RCSB:3aam, PDBe:3aam, PDBj:3aam
• PDBsum: 3aam
• PubMed: 21358045
• UniProt: Q5SK18