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1K3W

Crystal structure of a trapped reaction intermediate of the DNA Repair Enzyme Endonuclease VIII with DNA

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
A0003824molecular_functioncatalytic activity
A0003906molecular_functionDNA-(apurinic or apyrimidinic site) endonuclease activity
A0006281biological_processDNA repair
A0006284biological_processbase-excision repair
A0006974biological_processDNA damage response
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_idAC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE ZN A 501
ChainResidue
ACYS237
ACYS240
ACYS257
ACYS260

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 A 551
ChainResidue
AHOH918
AARG8
AASN12
AGLY213
AHOH627
AHOH906

site_idAC3
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 A 552
ChainResidue
AARG112
ALYS140
AALA191
AASP195
AHOH636
AHOH863
AHOH909
AHOH938

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 A 553
ChainResidue
AASN190
AALA191
AHOH610
AHOH866
AHOH915
AHOH946

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 Residues1
DetailsACT_SITE: Schiff-base intermediate with DNA
ChainResidueDetails
AGLU2

site_idSWS_FT_FI2
Number of Residues1
DetailsACT_SITE: Proton donor => ECO:0000305
ChainResidueDetails
AGLY3

site_idSWS_FT_FI3
Number of Residues1
DetailsACT_SITE: Proton donor; for beta-elimination activity => ECO:0000305
ChainResidueDetails
AALA53

site_idSWS_FT_FI4
Number of Residues1
DetailsACT_SITE: Proton donor; for delta-elimination activity => ECO:0000305
ChainResidueDetails
APRO253

site_idSWS_FT_FI5
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:11847126
ChainResidueDetails
ALEU70
AVAL125
ATYR169

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 2025-06-18

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