Het-PDB Navi2 (PDB: 6W3L)

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Ligands
Code	Name		Style	Show	Link
CA	Calcium ion				PoSSuM
NA	Sodium ion				PoSSuM

Non-standard Residues
Code	Name	Show
C7R	2'-deoxy-5'-O-thiophosphonocytidine

Glycosylation
Code	Name	Emphasize

Modification
Code	Name	Show

Download interaction data: 6W3L

Code :

6W3L PDBj RCSB PDB PDBe

Header :

DNA BINDING PROTEIN/DNA

Title :

APE1 exonuclease substrate complex wild-type

Release Data :

2020-06-10

Compound :

mol_id	molecule	chains
1	TCGACGGATCC	C

mol_id	molecule	chains
2	GCTGATGCG(C7R)	D

mol_id	molecule	chains
3	GGATCCGTCGATCGCATCAGC	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

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 ( 2.59 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

Chain :

A, B

UniProt :

P27695 (APEX1_HUMAN)

Reaction:	EC:	Evidence:
Reaction:	Physiological Direction:	Evidence:
a deoxyribonucleotide-2'-deoxyribose-5'-monophosphate-DNA + H2O = a 5'-end 2'-deoxyribose-5'-monophosphate-DNA + a 3'-end 2'- deoxyribonucleotide-DNA + H(+)	-	PubMed:15380100, PubMed:24079850, PubMed:8995436
	left-to-right	PubMed:19934257
Exonucleolytic cleavage in the 3'- to 5'-direction to yield nucleoside 5'-phosphates.	3.1.11.2	PubMed:11832948
	-	PubMed:11832948
a 3'-end 2'-deoxyribonucleotide-3'-phosphoglycolate-DNA + H2O = 2-phosphoglycolate + a 3'-end 2'-deoxyribonucleotide-DNA + H(+)	-	PubMed:7516064
	left-to-right	PubMed:7516064
a 3'-end 2'-deoxyribonucleotide-8-oxoguanine-DNA + H2O = 8- oxo-dGMP + a 3'-end 2'-deoxyribonucleotide-DNA + H(+)	-	PubMed:15831793
	left-to-right	PubMed:15831793
Cofactor:	Evidence:	Note:
Mn(2+)	ECO:0000269 \| PubMed:11286553 ECO:0000269 \| PubMed:19123919 ECO:0000269 \| PubMed:21762700 ECO:0000269 \| PubMed:24079850 ECO:0000269 \| PubMed:9804799 ECO:0000269 \| PubMed:11286553 ECO:0000269 \| PubMed:19123919 ECO:0000269 \| PubMed:21762700 ECO:0000269 \| PubMed:24079850 ECO:0000269 \| PubMed:9804799	Probably binds two magnesium or manganese ions per subunit.

PDB ID: 6W3L

Hetero Atom Contents

Structure summary

Reaction