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3S7W

Structure of the TvNiRb form of Thioalkalivibrio nitratireducens cytochrome c nitrite reductase with an oxidized Gln360 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
AHOH549
AHOH724
AHIS113
AHOH725
AHOH731
AHOH965
AHEC1006
AHOH1011
AALA114
AASP125
AHIS126
AVAL129
AARG131
ACYS184
ACYS187

site_idAC2
Number of Residues13
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
AHIS70
AGLN73
ALEU225
ACYS227
ACYS230
AHIS231
AMET384
ATYR395
ATHR396
AHIS398
AHOH812
AHOH836
AHEC1003

site_idAC3
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1006
ChainResidue
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
ACA525
AHOH532
AHOH577
AHOH719
AHEC1004
AHEC1007

site_idAC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
AGOL3
AHIS300
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
ACA525
AHOH719
AHOH720
AHOH732
AHOH894
AHEC1006
AHOH1025

site_idAC5
Number of Residues15
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418
AILE427
APHE490
AHOH607
AHOH992

site_idAC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ACYS35
ACYS38
AHIS39
ATHR59
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH936
AHOH949
AHEC1001
AHEC1003
ACYS14
APHE15
AHIS18
AHIS25
AVAL33
AASN34

site_idAC7
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ATHR68
ACYS69
AHIS70
AHIS231
AALA236
AHOH876
AHOH877
AHOH935
AHOH980
AHOH991
AHEC1002
AHEC1005
AHOH1072
BTHR68

site_idAC8
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC A 1001
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AHIS44
AVAL45
AALA48
ASER49
ASER50
AARG51
AARG51
AARG52
AMET53
AARG56
APRO57
ATHR59
AGLN275
AARG276
AHOH666
AHOH695
AHOH949
AHEC1002
AHOH1041
AHOH1057

site_idAC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE NO2 A 1
ChainResidue
APHE109
AARG131
ATYR303
AHIS361
AHOH730
AHOH965
AHEC1004
AHOH1011
AHOH1012

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 2
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH815
AHOH816

site_idBC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL A 3
ChainResidue
AARG96
AGLU115
APRO116
AASN486
ACA525
AHOH727
AHEC1007

site_idBC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE GOL A 4
ChainResidue
AASP101
AALA110
APHE111
AGLN175
ATRP444
AILE504
ALYS508
AHOH564
AHOH620

site_idBC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL A 524
ChainResidue
AGLN138
APHE139
AASN141
ATRP142

site_idBC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 525
ChainResidue
AGOL3
APRO116
AHOH595
AHOH894
AHEC1006
AHEC1007

site_idBC6
Number of Residues3
DetailsBINDING SITE FOR RESIDUE AZI A 526
ChainResidue
ASER76
AGLU79
ASER397

site_idBC7
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC B 1004
ChainResidue
BNO21
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BALA179
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BTYR303
BCYS305
BHIS361
BASN486
BHOH585
BHOH732
BHOH733
BHOH739
BHOH972
BHEC1006
BHOH1019

site_idBC8
Number of Residues16
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BHIS70
BGLN73
BLEU225
BCYS227
BCYS230
BHIS231
BMET384
BTYR395
BTHR396
BHIS398
BHOH598
BHOH820
BHOH844
BHOH930
BHOH946
BHEC1003

site_idBC9
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC B 1006
ChainResidue
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BMET229
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BCA526
BHOH571
BHOH596
BHOH727
BHEC1004
BHEC1007

site_idCC1
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BGOL3
BHIS300
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BARG404
BLYS431
BASN486
BPHE490
BHIS491
BCA526
BHOH727
BHOH728
BHOH902
BHEC1006

site_idCC2
Number of Residues16
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BHOH680
BHOH1000
BHOH1059

site_idCC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1002
ChainResidue
BCYS14
BPHE15
BHIS18
BILE21
BVAL33
BASN34
BCYS35
BCYS38
BHIS39
BLEU194
BPHE228
BPRO233
BHIS234
BARG239
BPHE274
BARG276
BARG282
BHEC1001
BHEC1003
BHOH1053
BHOH1055
BHOH1069

site_idCC4
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
BLYS29
BHIS30
BHIS37
BALA65
BCYS66
BTHR68
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH541
BHOH884
BHOH885
BHOH942
BHOH988
BHOH999
BHEC1002
BHEC1005

site_idCC5
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 1001
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BHIS44
BVAL45
BALA48
BSER49
BSER50
BARG52
BMET53
BARG56
BPRO57
BTHR59
BLEU194
BARG276
BGLY277
BHOH568
BHOH674
BHOH703
BHEC1002
BHOH1052

site_idCC6
Number of Residues7
DetailsBINDING SITE FOR RESIDUE NO2 B 1
ChainResidue
BTYR303
BHIS361
BHOH738
BHOH972
BHEC1004
BHOH1019
BHOH1020

site_idCC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 2
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH823
BHOH824

site_idCC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE GOL B 3
ChainResidue
BARG96
BGLU115
BPRO116
BASN486
BCA526
BHOH735
BHEC1007

site_idCC9
Number of Residues8
DetailsBINDING SITE FOR RESIDUE GOL B 4
ChainResidue
BASP101
BALA110
BGLN175
BTRP444
BILE504
BLYS508
BHOH591
BHOH633

site_idDC1
Number of Residues4
DetailsBINDING SITE FOR RESIDUE GOL B 524
ChainResidue
BGLN138
BPHE139
BASN141
BTRP142

site_idDC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE GOL B 525
ChainResidue
BASP168
BGLN169
BGLU213
BVAL214
BHOH754
BHOH768

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 526
ChainResidue
BGOL3
BPRO116
BHOH610
BHOH902
BHEC1006
BHEC1007

site_idDC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE AZI B 527
ChainResidue
BVAL58
BTHR59
BHOH589
BHOH703

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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