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2EA0

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli 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 Residues7
DetailsBINDING SITE FOR RESIDUE SO4 A 551
ChainResidue
AHOH832
AHOH840
AARG112
ALYS140
AALA191
AASP195
AHOH650

site_idAC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 C 552
ChainResidue
ALEU158
AHOH647
AHOH667
BHOH902
CDA429
CHOH652
CHOH845

site_idAC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE SO4 A 553
ChainResidue
AARG149
ALYS187

site_idAC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE SO4 A 554
ChainResidue
AARG8
AASN12
AHOH665
AHOH1053

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 A 555
ChainResidue
AASN190
AALA191
AHOH640
AHOH773
AHOH831
AHOH922

site_idAC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL A 511
ChainResidue
AARG124
AARG147
BDG401
BHOH682

Functional Information from PROSITE/UniProt
site_idPS01242
Number of Residues25
DetailsZF_FPG_1 Zinc finger FPG-type signature. Cer..CGsiIekttlss....RPfyWCpgCQ
ChainResidueDetails
ACYS237-GLN261

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
AARG252

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

Catalytic Information from CSA
site_idCSA1
Number of Residues4
DetailsAnnotated By Reference To The Literature 1k82
ChainResidueDetails
AGLU2
ALYS52
APRO1
AARG252

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PDB entries from 2024-10-09

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