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A second divalent metal ion in the active site of a new crystal form of human apurinic/apyrimidinic endonuclease, Ape1, and its implications for the catalytic mechanism

X-ray diffraction
2.2Å resolution
PDB entry 1e9n coloured by chain, front view.
PDB entry 1e9n coloured by chain, side view.
PDB entry 1e9n coloured by chain, top view.
Source organism: Homo sapiens
Assembly composition:
monomeric (preferred)
Entry contents: 1 distinct polypeptide molecule

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Assemblies

Assembly 1 (preferred)
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Assembly Name: DNA repair nuclease/redox regulator APEX1
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Multimeric state: monomeric
Accessible surface area: 12146.34 Å2
Buried surface area: 350.91 Å2
Dissociation area: 95.07 Å2
Dissociation energy (ΔGdiss): -2.8 kcal/mol
Dissociation entropy (TΔSdiss): 2.29 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-151054
Assembly 2
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Assembly Name: DNA repair nuclease/redox regulator APEX1
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Multimeric state: monomeric
Accessible surface area: 12097.67 Å2
Buried surface area: 347.24 Å2
Dissociation area: 93.96 Å2
Dissociation energy (ΔGdiss): -2.8 kcal/mol
Dissociation entropy (TΔSdiss): 2.29 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-151054

Macromolecules

DNA repair nuclease/redox regulator APEX1
Chains: A, B
Length: 318 amino acids
Theoretical weight: 35.61 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P27695 (Residues: 1-318; Coverage: 100%)
Gene names: APE, APE1, APEX, APEX1, APX, HAP1, REF1
Pfam: Endonuclease/Exonuclease/phosphatase family
InterPro:
CATH: Endonuclease/exonuclease/phosphatase
SCOP: DNase I-like
DNA repair nuclease/redox regulator APEX1 in PDB entry 1e9n, assembly 1, front view.
DNA repair nuclease/redox regulator APEX1 in PDB entry 1e9n, assembly 1, side view.
DNA repair nuclease/redox regulator APEX1 in PDB entry 1e9n, assembly 1, top view.
PDBe-KB: UniProt Coverage View: P27695  
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