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3OWM

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with hydroxylamine

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
ANO21
ALYS188
AARG242
ACYS299
AHIS300
ATYR303
ACYS305
AHIS361
AASN486
AHOH630
AHOH775
AHIS113
AHOH776
AHOH783
AHOH794
AHEC1006
AHOH1128
AALA114
AASP125
AHIS126
AVAL129
AARG131
ACYS184
ACYS187

site_idAC2
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
ACYS66
AHIS70
AGLN73
APHE74
ALEU225
AASN226
ACYS227
ACYS230
AHIS231
AMET384
ATYR395
ATHR396
AHIS398
AHOH746
AHOH878
AHOH901
AHOH991
AHEC1003
AHEC1006
AHOH1049

site_idAC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 1006
ChainResidue
ACA3
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
ALYS188
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
AHOH620
AHOH638
AHOH769
AHEC1004
AHEC1005
AHEC1007

site_idAC4
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
ACA3
AHIS300
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
AHOH769
AHOH770
AHOH771
AHOH784
AHEC1006
AHOH1077

site_idAC5
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
APHE490
APG4533
AHOH714
AHOH804
AHOH1050
AHOH1066
AHOH1102
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
AASN375
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418
AILE427

site_idAC6
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ACYS14
APHE15
AHIS18
AILE21
AHIS25
AVAL33
AASN34
ACYS35
ACYS38
AHIS39
ATHR59
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH550
AHOH705
AHOH739
AHEC1001
AHEC1003

site_idAC7
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ACYS69
AHIS70
ACYS227
AHIS231
AALA236
AHOH960
AHOH962
AHEC1002
AHEC1005
AHOH1021
AHOH1055
AHOH1141

site_idAC8
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC A 1001
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AHIS44
AVAL45
AALA48
ASER49
ASER50
AARG52
AMET53
AARG56
APRO57
ATHR59
ALEU194
AARG276
AGLY277
AHOH545
AHOH548
AHOH707
AHOH744
AHEC1002

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NO2 A 1
ChainResidue
ATYR303
AGLN360
AHIS361
AHOH782
AHEC1004
AHOH1128

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 2
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH881
AHOH882

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 3
ChainResidue
APRO116
AHOH645
AHOH652
AHEC1006
AHEC1007
AHOH1077

site_idBC3
Number of Residues16
DetailsBINDING SITE FOR RESIDUE TRS A 524
ChainResidue
ALYS102
ALYS102
ALYS102
AHOH665
AHOH665
AHOH665
AHOH976
AHOH976
AHOH976
AHOH1072
AHOH1072
AHOH1072
AHOH1082
AHOH1082
AHOH1082
AHOH1097

site_idBC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 525
ChainResidue
AHOH1068
AHOH1068
AHOH1068
AHOH1082
AHOH1082
AHOH1082

site_idBC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG6 A 526
ChainResidue
ATYR309
ALEU311
AGLY314
AARG348
AALA355
AHOH590
AHOH1016

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 A 527
ChainResidue
AGLN138
APHE139
ATRP142
AHOH951

site_idBC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG6 A 528
ChainResidue
ATHR94
ALYS431
AASN432
AHIS435
AHOH613
AHOH989

site_idBC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG6 A 529
ChainResidue
AALA31
AASN34
AHOH1075
BHOH561

site_idBC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 530
ChainResidue
AARG171
APHE172
ASER174

site_idCC1
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 A 531
ChainResidue
AASP62
AGLU64

site_idCC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 A 532
ChainResidue
AMET53
AGLY54
AGLU55
AARG56
AHOH611

site_idCC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 A 533
ChainResidue
AASN375
AASP381
AHOH539
AHEC1008

site_idCC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE NA A 4
ChainResidue
AHOH728
AHOH1098
BHEC1003

site_idCC5
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC B 1004
ChainResidue
BNO21
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BTYR303
BCYS305
BHIS361
BASN486
BHOH583
BHOH812
BHOH813
BHOH820
BHOH831
BHEC1006
BHOH1167

site_idCC6
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BCYS66
BHIS70
BGLN73
BPHE74
BLEU225
BASN226
BCYS227
BCYS230
BHIS231
BALA290
BMET384
BTYR395
BTHR396
BHIS398
BHOH783
BHOH915
BHOH938
BHEC1003
BHEC1006
BHOH1036
BHOH1088

site_idCC7
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1006
ChainResidue
BCA3
BHOH4
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BMET229
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BHOH591
BHOH806
BHEC1004
BHEC1005
BHEC1007

site_idCC8
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BCA3
BHIS300
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BARG404
BLYS431
BASN486
BPHE490
BHIS491
BHOH806
BHOH807
BHOH808
BHOH821
BHEC1006
BHOH1116

site_idCC9
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BASN375
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BHOH751
BHOH841
BHOH1089
BHOH1105
BHOH1141

site_idDC1
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 1002
ChainResidue
BCYS14
BPHE15
BHIS18
BILE21
BHIS25
BVAL33
BASN34
BCYS35
BCYS38
BHIS39
BILE193
BLEU194
BPHE228
BPRO233
BHIS234
BARG239
BPHE274
BARG276
BARG282
BHOH742
BHOH776
BHEC1001
BHEC1003

site_idDC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
ANA4
AHIS37
BLYS29
BHIS30
BVAL33
BHIS37
BALA65
BCYS66
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH551
BHOH638
BHOH997
BHOH999
BHEC1002
BHEC1005
BHOH1060
BHOH1094

site_idDC3
Number of Residues28
DetailsBINDING SITE FOR RESIDUE HEC B 1001
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BALA41
BHIS44
BVAL45
BALA48
BSER49
BSER50
BARG51
BARG51
BARG52
BMET53
BARG56
BPRO57
BTHR59
BLEU194
BGLN275
BARG276
BHOH625
BHOH626
BHOH628
BHOH744
BHOH776
BHOH781
BHEC1002

site_idDC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NO2 B 1
ChainResidue
BTYR303
BHIS361
BHOH819
BHEC1004
BHOH1167

site_idDC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 2
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH918
BHOH919

site_idDC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 3
ChainResidue
BPRO116
BHOH598
BHOH605
BHEC1006
BHEC1007
BHOH1116

site_idDC7
Number of Residues22
DetailsBINDING SITE FOR RESIDUE TRS B 524
ChainResidue
BLYS102
BLYS102
BLYS102
BHOH608
BHOH608
BHOH608
BHOH618
BHOH618
BHOH618
BHOH1021
BHOH1021
BHOH1021
BHOH1111
BHOH1111
BHOH1111
BHOH1121
BHOH1121
BHOH1121
BHOH1136
BHOH1164
BHOH1164
BHOH1164

site_idDC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 525
ChainResidue
BHOH1107
BHOH1107
BHOH1107
BHOH1121
BHOH1121
BHOH1121

site_idDC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG6 B 526
ChainResidue
BLEU311
BGLY314
BARG348
BALA355
BPG6527
BHOH1055

site_idEC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG6 B 527
ChainResidue
BTYR309
BARG348
BPG6526
BHOH921

site_idEC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 528
ChainResidue
BGLN138
BPHE139
BTRP142
BHOH672

site_idEC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG6 B 529
ChainResidue
BTHR94
BLYS431
BHIS435
BHOH680
BHOH683
BHOH1020

site_idEC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG6 B 530
ChainResidue
BALA31
BASN34
BHOH561
BHOH693
BHOH1114

site_idEC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 531
ChainResidue
BARG171
BPHE172
BSER174

site_idEC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 532
ChainResidue
BARG60
BASP62

site_idEC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 533
ChainResidue
BARG153
BASN222
BHOH1061

site_idEC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 B 534
ChainResidue
BLYS336
BGLN340
BGLU470
BTYR473
BHOH951

site_idEC9
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 535
ChainResidue
BGLN143
BCYS414
BHIS415
BGLU417

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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