Het-PDB Navi2 (PDB: 1HD7)

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Ligands
Code	Name		Style	Show	Link
PB	Lead (II) ion				PoSSuM

Non-standard Residues
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Glycosylation
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Download interaction data: 1HD7

Code :

1HD7 PDBj RCSB PDB PDBe

Header :

DNA REPAIR

Title :

A Second Divalent Metal Ion in the Active Site of a New Crystal Form of Human Apurinic/Apyridinimic Endonuclease, Ape1, and its Implications for the Catalytic Mechanism

Release Data :

2001-02-16

Compound :

mol_id	molecule	chains	synonym
1	DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE	A	AP ENDONUCLEASE 1, HAP1, REF1, APE1
	ec: 4.2.99.18

Source :

mol_id	organism_scientific	organism_common	expression_system
1	HOMO SAPIENS (taxid:9606)	HUMAN	ESCHERICHIA COLI (taxid:469008)
	tissue: ALL cell: ALL organelle: NUCLEUS expression_system_strain: BL21(DE3) expression_system_plasmid: PET11D expression_system_gene: APE1

Authors :

Beernink, P.T., Segelke, B.W., Rupp, B.

Keywords :

DNA REPAIR, ENDONUCLEASE, APE1, HAP1, REF-1

Exp. method :

X-RAY DIFFRACTION ( 1.95 Å )

Citation :

Two Divalent Metal Ions in the Active Site of a New Crystal Form of Human Apurinic/Apyrimidinic Endonuclease, Ape1: Implications for the Catalytic Mechanism

Beernink, P.T.,Segelke, B.W.,Hadi, M.Z. et al.
(2001) J.Mol.Biol. 307 : 1023

PubMed: 11286553
DOI: 10.1006/JMBI.2001.4529

Chain :

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: 1HD7

Hetero Atom Contents

Structure summary

Reaction