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3SCE

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with a covalent bond between the CE1 atom of Tyr303 and the CG atom of Gln360 (TvNiRb)

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 Residues23
DetailsBINDING SITE FOR RESIDUE HEC A 1004
ChainResidue
APO41
ALYS188
AARG242
ACYS299
AHIS300
ATYR303
ACYS305
AHIS361
AASN486
AHOH554
AHOH727
AHIS113
AHOH728
AHOH734
AHEC1006
AHOH1058
AALA114
AASP125
AHIS126
AVAL129
AARG131
ACYS184
ACYS187

site_idAC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
ACYS66
AHIS70
AGLN73
APHE74
ALEU225
AASN226
ACYS227
ACYS230
AHIS231
AALA290
AMET384
ATYR395
ATHR396
AHIS398
AHOH675
AHOH700
AHOH804
AHOH827
AHOH875
AHOH941
AHEC1003

site_idAC3
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1006
ChainResidue
ACA3
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
AHOH544
AHOH562
AHOH722
AHEC1004
AHEC1007

site_idAC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
ACA3
AHIS300
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
APG4533
AHOH722
AHOH723
AHOH731
AHOH735
AHOH888
AHEC1006

site_idAC5
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
APG4530
AHOH658
AHOH878
AHOH893
AHOH1060
AHOH1074
AHOH1086
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
AVAL377
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418
AILE427
APHE490

site_idAC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ACYS14
APHE15
AHIS18
AVAL33
AASN34
ACYS35
ACYS38
AHIS39
ATHR59
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH578
AHOH647
AHOH892
AHEC1001
AHEC1003

site_idAC7
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ACYS69
AHIS70
ACYS227
AHIS231
AALA236
AHOH643
AHOH875
AHOH990
AHEC1002
AHEC1005
AHOH1036
AHOH1038
AHOH1120
AHOH1129

site_idAC8
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC A 1001
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AHIS44
AALA48
ASER49
ASER50
AARG52
AMET53
AARG56
APRO57
ATHR59
ALEU194
AARG276
AGLY277
AHOH576
AHOH648
AHOH650
AHOH698
AHEC1002
AHOH1030

site_idAC9
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 A 1
ChainResidue
APHE109
AARG131
ATYR303
AGLN360
AHIS361
AHOH734
AHOH925
AHEC1004
AHOH1058
AHOH1059

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 2
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH807
AHOH808

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 3
ChainResidue
APRO116
AHOH571
AHOH582
AHOH888
AHEC1006
AHEC1007

site_idBC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 4
ChainResidue
AARG171
APHE172
ASER174

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG6 A 524
ChainResidue
AGLN138
APHE139
ATRP142
AASP494
AHOH939

site_idBC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG6 A 525
ChainResidue
ALEU311
AGLY314
AARG348
AALA355
AHOH822

site_idBC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 526
ChainResidue
AARG60
AASP62
AHOH653

site_idBC7
Number of Residues12
DetailsBINDING SITE FOR RESIDUE PO4 A 527
ChainResidue
AHOH585
AHOH585
AHOH585
AHOH901
AHOH901
AHOH901
AHOH913
AHOH913
AHOH913
AHOH950
AHOH950
AHOH950

site_idBC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 A 528
ChainResidue
ALEU88
AASN432
AHIS435
AHOH959
AHOH970

site_idBC9
Number of Residues1
DetailsBINDING SITE FOR RESIDUE PG4 A 529
ChainResidue
ATHR270

site_idCC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 530
ChainResidue
AASN375
AGLY376
AHEC1008

site_idCC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 531
ChainResidue
AMET53
AGLU55
AARG56

site_idCC3
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 A 532
ChainResidue
AARG153
AHOH606

site_idCC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 A 533
ChainResidue
AARG81
AARG404
ALYS431
AHEC1007
AHOH1061

site_idCC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE NA A 534
ChainResidue
AGLU390
AHOH1047
AHOH1130
BHOH1027

site_idCC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA A 535
ChainResidue
AGLU265
AASP288
AHOH897
AHOH1077
AHOH1108

site_idCC7
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC B 1004
ChainResidue
BPO41
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BVAL301
BTYR303
BCYS305
BHIS361
BASN486
BHOH667
BHOH788
BHOH789
BHOH795
BHEC1006
BHOH1114

site_idCC8
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BCYS66
BHIS70
BGLN73
BPHE74
BLEU225
BCYS227
BCYS230
BHIS231
BALA290
BMET384
BTYR395
BTHR396
BHIS398
BHOH761
BHOH865
BHOH888
BHOH933
BHOH997
BHEC1003
BHEC1006

site_idCC9
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1006
ChainResidue
BCA3
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BMET229
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BHOH637
BHOH675
BHOH783
BHEC1004
BHEC1005
BHEC1007

site_idDC1
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BCA3
BHIS300
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BARG404
BLYS431
BASN486
BPHE490
BHIS491
BHOH545
BHOH783
BHOH784
BHOH792
BHOH796
BHOH944
BHEC1006

site_idDC2
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BASN375
BVAL377
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BPG4530
BHOH546
BHOH555
BHOH739
BHOH935
BHOH949
BHOH1116

site_idDC3
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
BHOH557
BHOH732
BHEC1001
BHEC1003

site_idDC4
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
BLYS29
BHIS30
BVAL33
BHIS37
BALA65
BCYS66
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH578
BHOH597
BHOH933
BHEC1002
BHEC1005
BHOH1055
BHOH1093
BHOH1095

site_idDC5
Number of Residues26
DetailsBINDING SITE FOR RESIDUE HEC B 1001
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BHIS44
BVAL45
BALA48
BSER49
BARG51
BARG52
BMET53
BARG56
BPRO57
BTHR59
BLEU194
BGLN275
BARG276
BARG278
BHOH557
BHOH560
BHOH734
BHOH759
BHOH902
BHEC1002
BHOH1039

site_idDC6
Number of Residues10
DetailsBINDING SITE FOR RESIDUE PO4 B 1
ChainResidue
BPHE109
BARG131
BTYR303
BGLN360
BHIS361
BHOH795
BHOH981
BHEC1004
BHOH1114
BHOH1115

site_idDC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 2
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH868
BHOH869

site_idDC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 3
ChainResidue
BPRO116
BHOH688
BHOH698
BHOH944
BHEC1006
BHEC1007

site_idDC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 4
ChainResidue
BARG171
BPHE172
BSER174

site_idEC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG6 B 524
ChainResidue
BGLN138
BPHE139
BTRP142

site_idEC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG6 B 525
ChainResidue
BLEU311
BGLY314
BARG348
BALA355
BHOH883

site_idEC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE PO4 B 527
ChainResidue
BHOH701
BHOH701
BHOH701
BHOH957
BHOH957
BHOH957
BHOH969
BHOH969
BHOH1014
BHOH1014
BHOH1014

site_idEC4
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 528
ChainResidue
BTHR94
BHIS435

site_idEC5
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PG4 B 529
ChainResidue
BALA110
BPHE111
BGLN175
BTRP444
BLYS508
BHOH672
BHOH695
BHOH703
BHOH910

site_idEC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 530
ChainResidue
BASN375
BGLY376
BVAL377
BHEC1008

site_idEC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 B 531
ChainResidue
BGLN267
BTHR289
BALA290
BHOH861
BHOH1044

site_idEC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG4 B 532
ChainResidue
BLEU311
BLYS336
BGLN340
BGLU470
BTYR473
BHOH898
BHOH899

site_idEC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 533
ChainResidue
BARG153
BTHR157
BASN222

site_idFC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 B 534
ChainResidue
BLEU6
BVAL36
BHIS39
BASP40
BARG60

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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