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1Q3B

Crystal structure of the DNA repair enzyme endonuclease-VIII (Nei) from E. coli: The R252A mutant at 2.05 resolution.

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 301
ChainResidue
ACYS237
ACYS240
ACYS257
ACYS260

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 302
ChainResidue
AHIS184
AHIS262
AHIS262
AHOH530

site_idAC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MG A 303
ChainResidue
AHIS199
AHIS220
AHOH468
AASP195

site_idAC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE GOL A 351
ChainResidue
AASN12
AVAL76
AHOH526

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Schiff-base intermediate with DNA"}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues1
DetailsActive site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues1
DetailsActive site: {"description":"Proton donor; for beta-elimination activity","evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues3
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"11847126","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

239803

PDB entries from 2025-08-06

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