Brand  (β version)

PDB ID: 6W3U

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Ligands
Code Name Style Show Link
CA Calcium ion PoSSuM
EDO 1,2-ethanediol PoSSuM
Non-standard Residues
Code Name Show
C7R 2'-deoxy-5'-O-thiophosphonocytidine
C7S 2'-deoxy-5'-O-thiophosphonocytidine
Glycosylation
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Structure summary

Code : 6W3U   PDBj   RCSB PDB   PDBe
Header : DNA BINDING PROTEIN/DNA
Title : APE1 exonuclease substrate complex R237C
Release Data : 2020-06-10
Compound :
mol_id molecule chains
1 DNA (5'-D(P*TP*CP*GP*AP*CP*GP*GP*AP*TP*CP*C)-3') C
mol_id molecule chains
2 DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*GP*(C7R))-3') D
mol_id molecule chains
3 DNA (5'-D(*GP*GP*AP*TP*CP*CP*GP*TP*CP*GP*AP*TP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3') E
mol_id molecule chains synonym
4 DNA-(apurinic or apyrimidinic site) lyase A,B APEX nuclease,APEN,Apurinic-apyrimidinic endonuclease 1,APE-1,REF-1,Redox factor-1
ec: 3.1.-.-,4.2.99.18
mutation: R237C
Source :
mol_id organism_scientific
1 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
2 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific
3 Synthetic construct  (taxid:32630)
synthetic: yes
mol_id organism_scientific organism_common expression_system
4 Homo sapiens  (taxid:9606) Human Escherichia coli  (taxid:562)
gene: APEX1, APE, APE1, APEX, APX, HAP1, REF1
Authors : Freudenthal, B.D., Whitaker, A.M.
Keywords : nuclease, abasic site, DNA repair, DNA BINDING PROTEIN, DNA BINDING PROTEIN-DNA complex
Exp. method : X-RAY DIFFRACTION ( 2.40 Å )
Citation :

Molecular and structural characterization of disease-associated APE1 polymorphisms.

Whitaker, A.M.,Stark, W.J.,Flynn, T.S.  et al.
(2020)  DNA Repair (Amst.)  91-92 : 102867 - 102867

PubMed: 32454397
DOI: 10.1016/j.dnarep.2020.102867

Reaction

Chain : A, B
UniProt : P27695 (APEX1_HUMAN)
Reaction: EC: Evidence:
Physiological Direction:
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates. 3.1.11.2 PubMed:11286553, PubMed:15380100, PubMed:19123919, PubMed:21762700, PubMed:9804799
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