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2OPF

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli (R252A) in complex with AP-site containing DNA substrate

Functional Information from GO Data
ChainGOidnamespacecontents
A0000703molecular_functionoxidized pyrimidine nucleobase lesion DNA N-glycosylase activity
A0003676molecular_functionnucleic acid binding
A0003677molecular_functionDNA binding
A0003684molecular_functiondamaged DNA binding
A0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0008270molecular_functionzinc ion binding
A0016787molecular_functionhydrolase activity
A0016798molecular_functionhydrolase activity, acting on glycosyl bonds
A0016799molecular_functionhydrolase activity, hydrolyzing N-glycosyl compounds
A0016829molecular_functionlyase activity
A0019104molecular_functionDNA N-glycosylase activity
A0046872molecular_functionmetal ion binding
A0140078molecular_functionclass I DNA-(apurinic or apyrimidinic site) endonuclease activity
Functional Information from PDB Data
site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 501
ChainResidue
ACYS237
ACYS240
ACYS257
ACYS260

site_idAC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SO4 A 601
ChainResidue
AARG8
AASN12
AGLY213
AGLN214
AHOH1220

site_idAC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 701
ChainResidue
AGLN177
AALA196
AALA200
AGLU203
AHOH1137
AHOH1166
AHOH1176

site_idAC5
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL C 702
ChainResidue
BDA407
CDG424
CDG425
CDA426
CHOH1050
CHOH1070
CHOH1134
CHOH1163

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL A 703
ChainResidue
AALA9
AASN12
AASN68
ATRP74
AHOH1039
AHOH1153

site_idAC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 704
ChainResidue
AASP24
ATRP26
AGLN36
AGLY80
AGLU82
ALYS92
AHOH1123

site_idAC8
Number of Residues2
DetailsBINDING SITE FOR RESIDUE GOL A 705
ChainResidue
AARG75
AGLN84

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues34
DetailsZN_FING: FPG-type
ChainResidueDetails
ALYS228-HIS262

site_idSWS_FT_FI2
Number of Residues1
DetailsACT_SITE: Schiff-base intermediate with DNA
ChainResidueDetails
APRO1

site_idSWS_FT_FI3
Number of Residues1
DetailsACT_SITE: Proton donor => ECO:0000305
ChainResidueDetails
AGLU2

site_idSWS_FT_FI4
Number of Residues1
DetailsACT_SITE: Proton donor; for beta-elimination activity => ECO:0000305
ChainResidueDetails
ALYS52

site_idSWS_FT_FI5
Number of Residues1
DetailsACT_SITE: Proton donor; for delta-elimination activity => ECO:0000305
ChainResidueDetails
AALA252

site_idSWS_FT_FI6
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:11847126
ChainResidueDetails
AGLN69
AARG124
AASN168

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PDB entries from 2024-09-11

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