Structure of PDB 5dg0 Chain A Binding Site BS04

Receptor Information

>5dg0 Chain A (length=276) Species: 9606 (Homo sapiens)

ALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEEAPDIL
CLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQCPLKV
SYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQRWDEAF
RKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQERQGFGE
LLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLLSHSLL
PALCDSKIRSKALGSDHCPITLYLAL

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: 5dg0 Chain A Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5dg0 Capturing snapshots of APE1 processing DNA damage.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): G225 N229
• Binding residue (residue number reindexed from 1): G183 N187
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): N68 D70 E96 Y171 D210 N212 D283 D308 H309
• Catalytic site (residue number reindexed from 1): N26 D28 E54 Y129 D168 N170 D241 D266 H267
• Enzyme Commision number: 3.1.11.2: exodeoxyribonuclease III.
  3.1.21.-

Gene Ontology

Molecular Function

• GO:0003677 DNA binding
• GO:0003824 catalytic activity
• GO:0004518 nuclease activity
• GO:0004519 endonuclease activity

Biological Process

• GO:0006281 DNA repair

External links

• PDB: RCSB:5dg0, PDBe:5dg0, PDBj:5dg0
• PDBsum: 5dg0
• PubMed: 26458045
• UniProt: P27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)