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1Z4K

Structure of the D41N variant of the human mitochondrial deoxyribonucleotidase in complex with thymidine 3'-monophosphate

Functional Information from GO Data
ChainGOidnamespacecontents
A0008253molecular_function5'-nucleotidase activity
A0009264biological_processdeoxyribonucleotide catabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG A 229
ChainResidue
AASN41
AASP43
AASP176
AT3P4341
AHOH4430
AHOH4454

site_idAC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE T3P A 4341
ChainResidue
APHE49
APHE75
ATRP76
AVAL77
ATRP96
ATHR130
ASER131
APRO132
ALYS143
AMG229
AHOH4342
AHOH4346
AHOH4357
AHOH4371
AHOH4404
AHOH4405
AHOH4430
AHOH4454
AASN41
AMET42
AASP43

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsActive site: {"description":"Nucleophile"}
ChainResidueDetails

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

site_idSWS_FT_FI3
Number of Residues2
DetailsBinding site: {"evidences":[{"source":"PubMed","id":"12352955","evidenceCode":"ECO:0000269"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues8
DetailsBinding site: {}
ChainResidueDetails

Catalytic Information from CSA
site_idCSA1
Number of Residues2
DetailsAnnotated By Reference To The Literature 1q91
ChainResidueDetails
AASP43
AASN41

site_idMCSA1
Number of Residues3
DetailsM-CSA 812
ChainResidueDetails
AASN41covalently attached, metal ligand, nucleofuge, nucleophile
AASP43metal ligand
AASP176metal ligand

249697

PDB entries from 2026-02-25

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