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3UU9

Structure of the free TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase

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 601
ChainResidue
AHIS113
ALYS188
AARG242
ACYS299
AHIS300
ATYR303
ACYS305
AHIS361
AASN486
AHEC603
AHOH715
AALA114
AHOH756
AHOH759
AHOH788
AHOH1000
AASP125
AHIS126
AVAL129
AARG131
AALA179
ACYS184
ACYS187

site_idAC2
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC A 602
ChainResidue
ACYS66
AHIS70
AGLN73
APHE74
ALEU225
ACYS227
ACYS230
AHIS231
AALA290
AMET295
AMET384
ATYR395
ATHR396
AHIS398
AHEC603
AHEC607
AHOH928

site_idAC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 603
ChainResidue
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
ALYS188
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
AHEC601
AHEC602
AHEC604
ACA610
AHOH709
AHOH731
AHOH1048

site_idAC4
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC A 604
ChainResidue
AHIS300
AGLU363
APHE367
AHIS372
AVAL377
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
APRO403
AARG404
AILE427
ALYS431
AASN486
APHE490
AHIS491
AHEC603
ACA610
AHOH711
AHOH817
AHOH820
AHOH845
AHOH1043
AHOH1048

site_idAC5
Number of Residues16
DetailsBINDING SITE FOR RESIDUE HEC A 605
ChainResidue
AILE427
APHE490
AHOH806
AHOH1006
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
AASN375
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418

site_idAC6
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC A 606
ChainResidue
ACYS14
APHE15
AHIS18
AILE21
AHIS25
AVAL33
AASN34
ACYS35
ACYS38
AHIS39
AILE193
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHEC607
AHEC608
AHOH805
AHOH999
AHOH1060

site_idAC7
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC A 607
ChainResidue
ALYS29
AHIS30
AVAL33
AHIS37
AALA65
ACYS66
ACYS69
AHIS70
ACYS227
AHIS231
AALA236
AHEC602
AHEC606
AHOH1035
AHOH1135
BHIS37
BTHR68

site_idAC8
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 608
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AALA41
AHIS44
AVAL45
AALA48
ASER49
ASER50
AARG52
AARG56
APRO57
ATHR59
ALEU194
AARG276
AGLY277
AHEC606
AHOH814
AHOH819
AHOH1050

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 609
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH718
AHOH732

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 610
ChainResidue
APRO116
AHEC603
AHEC604
AHOH711
AHOH761
AHOH822

site_idBC2
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 611
ChainResidue
AGLY314
AARG348
APG4612

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE PG4 A 612
ChainResidue
ALEU311
AGLY314
AARG348
AALA355
APG4611
AHOH852

site_idBC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 613
ChainResidue
AGLN138
APHE139
ATRP142

site_idBC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 A 614
ChainResidue
AARG171
ASER174

site_idBC6
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 601
ChainResidue
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BALA179
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BTYR303
BCYS305
BHIS361
BASN486
BHEC603
BHOH732
BHOH770
BHOH773
BHOH803
BHOH1012

site_idBC7
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC B 602
ChainResidue
BCYS66
BHIS70
BGLN73
BLEU225
BASN226
BCYS227
BCYS230
BHIS231
BALA290
BMET384
BTYR395
BTHR396
BHIS398
BHEC603
BHEC607
BHOH862
BHOH942
BHOH1107

site_idBC8
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC B 603
ChainResidue
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BLYS188
BLEU225
BMET229
BMET295
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BGLN400
BHEC601
BHEC602
BHEC604
BCA610
BNA621
BHOH728
BHOH746

site_idBC9
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC B 604
ChainResidue
BHIS300
BGLU363
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BPRO403
BARG404
BILE427
BLYS431
BASN486
BPHE490
BHIS491
BHEC603
BCA610
BNA621
BHOH729
BHOH832
BHOH835
BHOH860
BHOH1055

site_idCC1
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC B 605
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BASN375
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BPG4616
BHOH821
BHOH1018
BHOH1100
BHOH1122

site_idCC2
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 606
ChainResidue
BCYS14
BPHE15
BHIS18
BILE21
BHIS25
BVAL33
BASN34
BCYS35
BCYS38
BHIS39
BILE193
BLEU194
BPHE228
BPRO233
BHIS234
BARG239
BPHE274
BARG276
BARG282
BHEC607
BHEC608
BHOH820
BHOH1011

site_idCC3
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC B 607
ChainResidue
AHIS37
BLYS29
BHIS30
BHIS37
BALA65
BCYS66
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHEC602
BHEC606
BHOH720
BHOH1047
BHOH1114
BHOH1115
BHOH1150

site_idCC4
Number of Residues27
DetailsBINDING SITE FOR RESIDUE HEC B 608
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BALA41
BHIS44
BVAL45
BALA48
BSER49
BSER50
BARG51
BARG51
BARG52
BMET53
BARG56
BPRO57
BTHR59
BLEU194
BGLN275
BARG276
BHEC606
BHOH829
BHOH834
BHOH945
BHOH1011
BHOH1079

site_idCC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 609
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH733
BHOH747

site_idCC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 610
ChainResidue
BPRO116
BHEC603
BHEC604
BHOH729
BHOH775
BHOH837

site_idCC7
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 B 611
ChainResidue
BLEU311
BARG348
BALA355
BPG4612
BHOH867

site_idCC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 612
ChainResidue
BGLY314
BARG348
BPG4611
BHOH1076

site_idCC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 613
ChainResidue
BGLN138
BPHE139
BTRP142

site_idDC1
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 614
ChainResidue
BARG171
BPHE172
BSER174

site_idDC2
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 615
ChainResidue
BTHR94
BSER95
BHIS435
BHOH703

site_idDC3
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 B 616
ChainResidue
BASN375
BGLY376
BASP381
BCYS414
BHEC605

site_idDC4
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 617
ChainResidue
BARG153
BTHR157
BHOH1034

site_idDC5
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 618
ChainResidue
BARG374
BHOH933

site_idDC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE PG4 B 619
ChainResidue
BHIS107
BGLY108
BALA177
BTHR178
BALA179
BHOH1014
BHOH1073

site_idDC7
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 B 620
ChainResidue
BPHE333
BLYS506
BHOH1070

site_idDC8
Number of Residues5
DetailsBINDING SITE FOR RESIDUE NA B 621
ChainResidue
BSER84
BARG401
BTHR402
BHEC603
BHEC604

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 2024-07-17

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