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3FO3

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase reduced by sodium dithionite (sulfite complex)

Functional Information from GO Data
ChainGOidnamespacecontents
A0005509molecular_functioncalcium ion binding
A0016491molecular_functionoxidoreductase activity
A0020037molecular_functionheme binding
A0042128biological_processnitrate assimilation
A0042279molecular_functionnitrite reductase (cytochrome, ammonia-forming) activity
A0042597cellular_componentperiplasmic space
A0046872molecular_functionmetal ion binding
A0097164biological_processammonium ion metabolic process
B0005509molecular_functioncalcium ion binding
B0016491molecular_functionoxidoreductase activity
B0020037molecular_functionheme binding
B0042128biological_processnitrate assimilation
B0042279molecular_functionnitrite reductase (cytochrome, ammonia-forming) activity
B0042597cellular_componentperiplasmic space
B0046872molecular_functionmetal ion binding
B0097164biological_processammonium ion metabolic process
Functional Information from PDB Data
site_idAC1
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC A 1004
ChainResidue
AHIS113
ALYS188
AARG242
ACYS299
AHIS300
ATYR303
ACYS305
AHIS361
AASN486
ASO3526
AHOH599
AALA114
AHOH713
AHOH856
AHOH857
AHOH863
AHEC1006
AASP125
AHIS126
AVAL129
AARG131
AALA179
ACYS184
ACYS187

site_idAC2
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
ACYS66
AHIS70
AGLN73
APHE74
ALEU225
AASN226
ACYS227
ACYS230
AHIS231
AALA290
AMET384
ATYR395
ATHR396
AHIS398
AHOH826
AHOH951
AHOH977
AHEC1003
AHEC1006
AHOH1065
AHOH1098
AHOH1112
AHOH1186
AHOH1187

site_idAC3
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1006
ChainResidue
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
ACA528
AHOH703
AHOH720
AHOH850
AHEC1004
AHEC1005
AHEC1007

site_idAC4
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
AARG96
AHIS300
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
ACA528
AHOH733
AHOH850
AHOH851
AHOH852
AHOH860
AHOH864
AHEC1006
AHEC1008
AHOH1146

site_idAC5
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
ACYS411
ACYS414
AHIS415
ATRP418
AILE427
APHE490
AHOH795
AHEC1007
AHOH1114
AHOH1128
AHOH1171
AHOH1194
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
AALA410

site_idAC6
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ACYS14
APHE15
AHIS18
AILE21
AVAL33
AASN34
ACYS35
ACYS38
AHIS39
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH786
AHEC1001
AHEC1003
AHOH1174

site_idAC7
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ATHR68
ACYS69
AHIS70
ACYS227
AHIS231
AALA236
AHOH573
AHOH586
AHOH677
AHOH678
AHEC1002
AHEC1005
AHOH1041
AHOH1207
AHOH1239

site_idAC8
Number of Residues27
DetailsBINDING SITE FOR RESIDUE HEC A 1001
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AHIS44
AVAL45
AALA48
ASER49
ASER50
AARG52
AMET53
AARG56
APRO57
ATHR59
ALEU194
AGLN275
AARG276
AHOH789
AHOH824
AHOH993
AHOH994
AHEC1002
AHOH1064
AHOH1068
AHOH1126
AHOH1174

site_idAC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SO3 A 526
ChainResidue
APHE109
AARG131
ATYR303
AGLN360
AHIS361
AHOH599
AHOH863
AHEC1004
AHOH1140

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 527
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH954
AHOH955

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 528
ChainResidue
APRO116
AHOH726
AHOH733
AHEC1006
AHEC1007
AHOH1146

site_idBC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO4 A 529
ChainResidue
AHIS18
ATHR19
AGLN20
AILE21
APHE274
AHOH785
AHOH1174

site_idBC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE THJ A 530
ChainResidue
AARG457
AARG457
AARG457
AHOH585
AHOH585
AHOH585
AHOH986
AHOH986
AHOH986

site_idBC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE NA A 531
ChainResidue
AHOH554
AHOH554
AHOH554
AHOH1132
AHOH1132
AHOH1132
AHOH1167
AHOH1167
AHOH1167

site_idBC6
Number of Residues13
DetailsBINDING SITE FOR RESIDUE PG6 A 532
ChainResidue
ATYR309
ALEU311
AGLY314
AARG348
AALA354
AALA355
AGLU470
AHOH673
AHOH674
AHOH968
AHOH971
AHOH990
AHOH1225

site_idBC7
Number of Residues18
DetailsBINDING SITE FOR RESIDUE TRS A 533
ChainResidue
AMET99
ALYS102
ALYS102
AHOH554
AHOH554
AHOH554
AHOH590
AHOH590
AHOH590
AHOH736
AHOH736
AHOH736
AHOH745
AHOH745
AHOH745
AHOH1167
AHOH1167
AHOH1167

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG6 A 534
ChainResidue
AALA11
AMET12
AALA31
AASN34
AHOH1143
BPG6535

site_idBC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG4 A 535
ChainResidue
AGLN138
APHE139
ATRP142
AHOH563
AHOH624
AHOH672
AHOH1151

site_idCC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG6 A 536
ChainResidue
APHE333
AGLU498
ALYS506
AHOH668
AHOH1107
AHOH1115

site_idCC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 A 537
ChainResidue
APRO307
AHOH577
AHOH578
AHOH676

site_idCC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 A 538
ChainResidue
AASN375
AGLY376
AHOH940
AHOH1197
AHOH1217

site_idCC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 539
ChainResidue
AARG171
APHE172
ASER174

site_idCC5
Number of Residues1
DetailsBINDING SITE FOR RESIDUE PG4 A 540
ChainResidue
APG4541

site_idCC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 A 541
ChainResidue
AGLN20
AMET24
AVAL272
APG4540
AHOH632

site_idCC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG6 A 542
ChainResidue
AASP320
AASP321
AHOH597

site_idCC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PG6 A 543
ChainResidue
ATHR351
ALYS447
AVAL511
AASN515
AHOH756
AHOH1035
AHOH1073
AHOH1156

site_idCC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA A 544
ChainResidue
AHOH598
AHOH749
AHOH852
AHOH1050
AHOH1146

site_idDC1
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC B 1004
ChainResidue
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BALA179
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BTYR303
BCYS305
BHIS361
BASN486
BSO3526
BPG4547
BHOH599
BHOH637
BHOH862
BHOH863
BHOH869
BHEC1006

site_idDC2
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BHIS70
BGLN73
BPHE74
BLEU225
BASN226
BCYS227
BCYS230
BHIS231
BALA290
BMET384
BTYR395
BTHR396
BHIS398
BHOH832
BHOH957
BHOH983
BHEC1003
BHEC1006
BHOH1072
BHOH1104
BHOH1118
BHOH1192
BHOH1193

site_idDC3
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1006
ChainResidue
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BMET229
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BCA528
BHOH627
BHOH643
BHOH856
BHEC1004
BHEC1005
BHEC1007

site_idDC4
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BARG96
BHIS300
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BARG404
BLYS431
BASN486
BPHE490
BHIS491
BCA528
BHOH656
BHOH856
BHOH857
BHOH858
BHOH866
BHOH870
BHEC1006
BHEC1008
BHOH1152

site_idDC5
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BPG4540
BHOH801
BHEC1007
BHOH1120
BHOH1134
BHOH1177
BHOH1200

site_idDC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1002
ChainResidue
BCYS14
BPHE15
BHIS18
BILE21
BHIS25
BVAL33
BASN34
BCYS35
BCYS38
BHIS39
BLEU194
BPHE228
BPRO233
BHIS234
BARG239
BPHE274
BARG276
BARG282
BHOH792
BHEC1001
BHEC1003
BHOH1180

site_idDC7
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
BLYS29
BHIS30
BHIS37
BALA65
BCYS66
BTHR68
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH573
BHOH586
BHOH609
BHEC1002
BHEC1005
BHOH1048
BHOH1213

site_idDC8
Number of Residues28
DetailsBINDING SITE FOR RESIDUE HEC B 1001
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BHIS44
BVAL45
BALA48
BSER49
BARG51
BARG51
BARG52
BMET53
BARG56
BPRO57
BTHR59
BLEU194
BGLN275
BARG276
BHOH758
BHOH795
BHOH830
BHEC1002
BHOH1009
BHOH1071
BHOH1074
BHOH1132
BHOH1180

site_idDC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SO3 B 526
ChainResidue
BPHE109
BARG131
BTYR303
BGLN360
BHIS361
BHOH599
BHOH869
BHEC1004
BHOH1146

site_idEC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 527
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH960
BHOH961

site_idEC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 528
ChainResidue
BPRO116
BHOH649
BHOH656
BHEC1006
BHEC1007
BHOH1152

site_idEC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE SO3 B 529
ChainResidue
BHIS18
BTHR19
BGLN20
BILE21
BPHE274
BHOH689
BHOH1180

site_idEC4
Number of Residues9
DetailsBINDING SITE FOR RESIDUE THJ B 530
ChainResidue
BARG457
BARG457
BARG457
BHOH585
BHOH585
BHOH585
BHOH992
BHOH992
BHOH992

site_idEC5
Number of Residues12
DetailsBINDING SITE FOR RESIDUE NA B 531
ChainResidue
BTRS533
BTRS533
BTRS533
BHOH554
BHOH554
BHOH554
BHOH1138
BHOH1138
BHOH1138
BHOH1173
BHOH1173
BHOH1173

site_idEC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PG6 B 532
ChainResidue
BTYR309
BLEU311
BGLY314
BARG348
BALA354
BALA355
BHOH974
BHOH977
BHOH996
BHOH1231

site_idEC7
Number of Residues23
DetailsBINDING SITE FOR RESIDUE TRS B 533
ChainResidue
BLYS102
BLYS102
BNA531
BNA531
BNA531
BHOH554
BHOH554
BHOH554
BHOH590
BHOH590
BHOH590
BHOH659
BHOH659
BHOH659
BHOH668
BHOH668
BHOH668
BHOH702
BHOH702
BHOH702
BHOH1173
BHOH1173
BHOH1173

site_idEC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 B 534
ChainResidue
ASER50
AARG51
AARG278
AHOH622
BARG252
BGLU341
BHOH973
BHOH1051

site_idEC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG6 B 535
ChainResidue
ATHR32
APG6534
BALA11
BALA31
BTHR32
BASN34
BHOH1149

site_idFC1
Number of Residues8
DetailsBINDING SITE FOR RESIDUE PG4 B 536
ChainResidue
BGLN138
BPHE139
BTRP142
BASP494
BHOH563
BHOH1041
BHOH1156
BHOH1157

site_idFC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 537
ChainResidue
BPRO307
BTYR309
BHOH577
BHOH578

site_idFC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE PG4 B 538
ChainResidue
BTHR94
BSER95
BARG96
BGLU115
BHIS435
BHOH703
BHOH712
BHOH1141
BHOH1143
BHOH1144
BHOH1145
BHOH1154
BHOH1165

site_idFC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG4 B 539
ChainResidue
BMET53
BALA205
BARG276
BHOH756
BHOH788
BHOH913
BHOH1132

site_idFC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG4 B 540
ChainResidue
BASN375
BGLY376
BNA549
BHOH744
BHOH745
BHOH746
BHEC1008

site_idFC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 541
ChainResidue
BARG171
BPHE172

site_idFC7
Number of Residues1
DetailsBINDING SITE FOR RESIDUE PG6 B 542
ChainResidue
BHOH780

site_idFC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 543
ChainResidue
BASN141
BGLN143
BLYS144
BHOH890

site_idFC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG4 B 544
ChainResidue
BTHR351
BLYS447
BASN515
BHOH704
BHOH705
BHOH1162

site_idGC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 545
ChainResidue
BASP62
BGLU64

site_idGC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE ACT B 546
ChainResidue
BARG457
BASN515
BILE518
BASP519
BHOH705
BHOH1209

site_idGC3
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PG4 B 547
ChainResidue
BALA179
BALA180
BASN181
BASN306
BPRO307
BMET319
BHOH808
BHOH903
BHEC1004
BHOH1092

site_idGC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 548
ChainResidue
BHOH598
BHOH672
BHOH858
BHOH1057
BHOH1152

site_idGC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 549
ChainResidue
BASN375
BPG4540
BHOH722
BHOH723
BHOH783

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues32
DetailsBINDING: covalent => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y
ChainResidueDetails
ACYS14
ACYS230
ACYS296
ACYS299
ACYS379
ACYS382
ACYS411
ACYS414
BCYS14
BCYS17
BCYS35
ACYS17
BCYS38
BCYS66
BCYS69
BCYS184
BCYS187
BCYS227
BCYS230
BCYS296
BCYS299
BCYS379
ACYS35
BCYS382
BCYS411
BCYS414
ACYS38
ACYS66
ACYS69
ACYS184
ACYS187
ACYS227

site_idSWS_FT_FI2
Number of Residues28
DetailsBINDING: axial binding residue => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y
ChainResidueDetails
AHIS18
AHIS372
AHIS383
AHIS398
AHIS415
AHIS491
BHIS18
BHIS30
BHIS39
BHIS44
BHIS70
AHIS30
BHIS119
BLYS188
BHIS234
BHIS300
BHIS372
BHIS383
BHIS398
BHIS415
BHIS491
AHIS39
AHIS44
AHIS70
AHIS119
ALYS188
AHIS234
AHIS300

site_idSWS_FT_FI3
Number of Residues2
DetailsBINDING: axial binding residue => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743
ChainResidueDetails
AHIS231
BHIS231

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: BINDING => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:20944237, ECO:0000269|PubMed:22281743, ECO:0007744|PDB:4L38, ECO:0007744|PDB:4L3X, ECO:0007744|PDB:4L3Y
ChainResidueDetails
AGLU302
ATYR303
ALYS358
AGLN360
BGLU302
BTYR303
BLYS358
BGLN360

site_idSWS_FT_FI5
Number of Residues4
DetailsCROSSLNK: 3'-(S-cysteinyl)-tyrosine (Tyr-Cys) => ECO:0000269|PubMed:19393666, ECO:0000269|PubMed:22281743
ChainResidueDetails
ATYR303
ACYS305
BTYR303
BCYS305

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PDB entries from 2024-07-24

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