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2JIQ

A New Catalytic Mechanism of Periplasmic Nitrate Reductase from Desulfovibrio desulfuricans ATCC 27774 from Crystallographic and EPR Data and based on detailed analysis of the sixth ligand

Functional Information from GO Data
ChainGOidnamespacecontents
A0005506molecular_functioniron ion binding
A0006777biological_processMo-molybdopterin cofactor biosynthetic process
A0008940molecular_functionnitrate reductase activity
A0009055molecular_functionelectron transfer activity
A0016491molecular_functionoxidoreductase activity
A0030151molecular_functionmolybdenum ion binding
A0042128biological_processnitrate assimilation
A0042597cellular_componentperiplasmic space
A0043546molecular_functionmolybdopterin cofactor binding
A0046872molecular_functionmetal ion binding
A0050140molecular_functionnitrate reductase (cytochrome) activity
A0051539molecular_function4 iron, 4 sulfur cluster binding
Functional Information from PDB Data
site_idAC1
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SF4 A 800
ChainResidue
ACYS13
ATYR15
ACYS16
AGLY19
ACYS20
ALEU46
ACYS47
APRO182
AVAL183

site_idAC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE MO A 810
ChainResidue
ACYS140
AMGD811
AMGD812
AUNX813

site_idAC3
Number of Residues30
DetailsBINDING SITE FOR RESIDUE MGD A 811
ChainResidue
AARG14
AGLN111
AASN136
ACYS140
AGLN312
AGLU416
ATHR417
AASN418
ATHR422
AILE443
AGLU444
APHE446
APRO461
AALA462
APHE463
ASER615
AARG617
ATRP622
AHIS623
ATHR624
ATHR626
APHE689
AASN697
ATYR713
ALYS714
AMO810
AMGD812
AUNX813
AHOH2487
AHOH2738

site_idAC4
Number of Residues36
DetailsBINDING SITE FOR RESIDUE MGD A 812
ChainResidue
ACYS16
ALYS49
ACYS140
AILE173
AGLY174
ASER175
AASN176
AGLU179
AALA180
AASP204
APRO205
AARG206
APRO222
AGLY223
AASP225
ACYS307
AMET308
AGLY309
AARG313
AGLY345
AGLN346
ATHR614
AMET616
AARG617
AVAL618
AILE619
AHIS621
ATRP622
AHIS623
ALYS714
AMO810
AMGD811
AHOH2220
AHOH2739
AHOH2740
AHOH2741

site_idAC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE UNX A 813
ChainResidue
ACYS140
AMET141
AGLN346
AMO810
AMGD811

site_idAC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NO2 A 814
ChainResidue
AMET616
AVAL618
AHIS621
APHE689
APHE690

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NO3 A 815
ChainResidue
ATHR150
AARG596
AVAL707
AHOH2742
AHOH2743
AHOH2744

site_idAC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE NO3 A 816
ChainResidue
AHOH2403
AHOH2746
AHOH2747
AVAL145
AARG354
ALEU362
ATYR533

site_idAC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NO3 A 817
ChainResidue
AGLY146
AVAL149
ATHR150
AVAL707
ANO3818

site_idBC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE NO3 A 818
ChainResidue
AALA142
AGLY146
AHIS361
AVAL707
ANO3817
ANO3819
AHOH2747

site_idBC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE NO3 A 819
ChainResidue
AARG138
AHIS361
AVAL707
AARG709
ANO3818
AHOH2749
AHOH2750

site_idBC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NO3 A 820
ChainResidue
ATHR150
AMET254
ALYS586
AVAL592
ATRP594

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues13
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01630, ECO:0000269|PubMed:10368307, ECO:0000269|PubMed:18327621, ECO:0007744|PDB:2JIM, ECO:0007744|PDB:2JIO, ECO:0007744|PDB:2JIP, ECO:0007744|PDB:2JIQ, ECO:0007744|PDB:2JIR, ECO:0007744|PDB:2NAP, ECO:0007744|PDB:2V3V, ECO:0007744|PDB:2V45
ChainResidueDetails
ACYS13
AASN418
ASER615
AASN697
ALYS714
ACYS16
ACYS20
ACYS47
AGLN111
AASN136
ACYS140
AGLY223
AMET308

site_idSWS_FT_FI2
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01630, ECO:0000269|PubMed:10368307, ECO:0000269|PubMed:18327621, ECO:0007744|PDB:2JIM, ECO:0007744|PDB:2JIP, ECO:0007744|PDB:2JIR, ECO:0007744|PDB:2NAP, ECO:0007744|PDB:2V3V, ECO:0007744|PDB:2V45
ChainResidueDetails
ALYS49

site_idSWS_FT_FI3
Number of Residues3
DetailsBINDING: BINDING => ECO:0000269|PubMed:10368307, ECO:0000269|PubMed:18327621, ECO:0007744|PDB:2JIM, ECO:0007744|PDB:2JIO, ECO:0007744|PDB:2JIP, ECO:0007744|PDB:2JIQ, ECO:0007744|PDB:2JIR, ECO:0007744|PDB:2NAP, ECO:0007744|PDB:2V3V, ECO:0007744|PDB:2V45
ChainResidueDetails
AASN176
AASP204
AILE443

site_idSWS_FT_FI4
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01630, ECO:0000269|PubMed:10368307, ECO:0000269|PubMed:18327621, ECO:0007744|PDB:2JIM, ECO:0007744|PDB:2JIP, ECO:0007744|PDB:2JIQ, ECO:0007744|PDB:2JIR, ECO:0007744|PDB:2NAP, ECO:0007744|PDB:2V3V, ECO:0007744|PDB:2V45
ChainResidueDetails
AGLN312

site_idSWS_FT_FI5
Number of Residues1
DetailsBINDING: BINDING => ECO:0000305|PubMed:18327621, ECO:0007744|PDB:2JIQ, ECO:0007744|PDB:2JIR
ChainResidueDetails
AMET616

site_idSWS_FT_FI6
Number of Residues1
DetailsBINDING: BINDING => ECO:0000255|HAMAP-Rule:MF_01630, ECO:0000305|PubMed:18327621, ECO:0007744|PDB:2JIQ, ECO:0007744|PDB:2JIR
ChainResidueDetails
APHE689

Catalytic Information from CSA
site_idCSA1
Number of Residues1
DetailsAnnotated By Reference To The Literature 1tmo
ChainResidueDetails
ACYS140

site_idCSA2
Number of Residues1
DetailsAnnotated By Reference To The Literature 1tmo
ChainResidueDetails
AARG138

226707

PDB entries from 2024-10-30

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