Structure of PDB 4qh9 Chain A Binding Site BS01

Receptor Information

>4qh9 Chain A (length=281) Species: 9606 (Homo sapiens)

ASEGPALYEDPPDQKTSPSGKPATLKICSWNVDGLRAWIKKKGLDWVKEE
APDILCLQETKCSENKLPAELQELPGLSHQYWSAPSDKEGYSGVGLLSRQ
APLKVSYGIGDEEHDQEGRVIVAEFDSFVLVTAYVPNAGRGLVRLEYRQR
WDEAFRKFLKGLASRKPLVLCGDLNVAHEEIDLRNPKGNKKNAGFTPQER
QGFGELLQAVPLADSFRHLYPNTPYAYTFWTYMMNARSKNVGWRLDYFLL
SHSLLPALCDSKIRSKALGSDHCPITLYLAL

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: 4qh9 Chain A Residue 408

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4qh9 High-resolution crystal structures reveal plasticity in the metal binding site of apurinic/apyrimidinic endonuclease I.
• Resolution: 2.175 Å
• Binding residue (original residue number in PDB): D70 E96
• Binding residue (residue number reindexed from 1): D33 E59
• 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): N31 D33 E59 Y134 D173 N175 D246 D271 H272
• 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:4qh9, PDBe:4qh9, PDBj:4qh9
• PDBsum: 4qh9
• PubMed: 25251148
• UniProt: P27695|APEX1_HUMAN DNA repair nuclease/redox regulator APEX1 (Gene Name=APEX1)