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2JAU

Crystal structure of D41N variant of human mitochondrial 5'(3')- deoxyribonucleotidase (mdN) in complex with 3'-azidothymidine 5'- 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 A1228
ChainResidue
AALA119
ALEU121
ATHR124
AHOH2085
AHOH2091
AHOH2092

site_idAC2
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PO4 A1229
ChainResidue
ATHR130
ASER131
AATM1230
AMG1231
AHOH2199
AHOH2202
AASN41
AMET42
AASP43

site_idAC3
Number of Residues26
DetailsBINDING SITE FOR RESIDUE ATM A1230
ChainResidue
AASN41
AASP43
APHE49
APHE75
ATRP76
AVAL77
ASER78
ATRP96
APHE102
ASER131
APRO132
AILE133
ACYS139
ALYS143
ALYS165
APO41229
AMG1231
AHOH2100
AHOH2140
AHOH2141
AHOH2199
AHOH2200
AHOH2201
AHOH2202
AHOH2203
AHOH2204

site_idAC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE MG A1231
ChainResidue
AASN41
AASP43
AASP176
APO41229
AATM1230
AHOH2140
AHOH2141

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues1
DetailsACT_SITE: Nucleophile
ChainResidueDetails
AASN41

site_idSWS_FT_FI2
Number of Residues1
DetailsACT_SITE: Proton donor => ECO:0000305
ChainResidueDetails
AASP43

site_idSWS_FT_FI3
Number of Residues2
DetailsBINDING: BINDING => ECO:0000269|PubMed:12352955
ChainResidueDetails
AASN41
AASP176

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING:
ChainResidueDetails
AASP43
APHE49
APHE75
ATRP76
AVAL77
ATRP96
ATHR130
ALYS165

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

222415

PDB entries from 2024-07-10

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