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3RKH

Structure of the Thioalkalivibrio nitratireducens cytochrome c nitrite reductase in a complex with nitrite (full occupancy)

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
ANO21
ACYS187
ALYS188
AARG242
ACYS299
AHIS300
ATYR303
ACYS305
AHIS361
AASN486
AHOH755
AHIS113
AHOH867
AHOH868
AHOH874
AHEC1006
AALA114
AASP125
AHIS126
AVAL129
AARG131
AALA179
ACYS184

site_idAC2
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
ACYS66
AHIS70
AGLN73
APHE74
ALEU225
ACYS227
ACYS230
AHIS231
AALA290
AMET384
ATYR395
ATHR396
AHIS398
AHOH572
AHOH716
AHOH842
AHOH951
AHOH972
AHEC1003

site_idAC3
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC A 1006
ChainResidue
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
ALYS188
ALEU225
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
AGLN400
AARG401
AHOH737
AHOH763
AHOH862
AHEC1004
AHEC1007
AHOH1054

site_idAC4
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
AHIS300
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
AHOH862
AHOH871
AHEC1006
AHOH1054
AHOH1071

site_idAC5
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
AHOH601
AHOH1117
ATRP142
AGLN143
AVAL371
AHIS372
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418
AILE427
APHE490
APRO493
AHOH581
AHOH584

site_idAC6
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ACYS14
APHE15
AHIS18
AILE21
AHIS25
AVAL33
AASN34
ACYS35
ACYS38
AHIS39
ATHR59
AILE193
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH613
AHOH814
AHEC1001
AHEC1003
AHOH1059

site_idAC7
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ACYS69
AHIS70
ACYS227
AHIS231
AALA236
AHOH525
AHOH651
AHEC1002
AHEC1005
AHOH1068
AHOH1096
AHOH1186

site_idAC8
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC A 1001
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AALA41
AHIS44
AVAL45
AALA48
ASER49
ASER50
AARG52
AMET53
AARG56
APRO57
ATHR59
ALEU194
AARG276
AGLY277
AHOH528
AHOH614
AHOH816
AHOH840
AHEC1002
AHOH1153

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NO2 A 1
ChainResidue
APHE109
AARG131
ATYR303
AHIS361
AHEC1004
AHOH1073

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 2
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH954
AHOH955

site_idBC2
Number of Residues8
DetailsBINDING SITE FOR RESIDUE MRD A 3
ChainResidue
AARG87
AVAL128
AGLN138
APHE139
ATRP142
AVAL145
AARG497
AHOH625

site_idBC3
Number of Residues22
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
BHOH772
BHOH884
BHOH885
BHOH891
BHEC1006

site_idBC4
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BCYS66
BHIS70
BGLN73
BPHE74
BLEU225
BASN226
BCYS227
BCYS230
BHIS231
BALA290
BMET384
BTYR395
BTHR396
BHIS398
BHOH572
BHOH728
BHOH732
BHOH859
BHOH968
BHOH989
BHEC1003
BHEC1006

site_idBC5
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC B 1006
ChainResidue
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BLYS188
BLEU225
BMET229
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BGLN400
BARG401
BHOH761
BHOH780
BHOH879
BHEC1004
BHEC1005
BHEC1007
BHOH1071

site_idBC6
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BHIS300
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BPRO403
BARG404
BILE427
BLYS431
BASN486
BPHE490
BHIS491
BHOH879
BHOH880
BHOH888
BHEC1006
BHOH1071
BHOH1087

site_idBC7
Number of Residues15
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BTRP142
BGLN143
BVAL371
BHIS372
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BHOH531
BHOH581
BHOH1133

site_idBC8
Number of Residues24
DetailsBINDING SITE FOR RESIDUE HEC B 1002
ChainResidue
BCYS14
BPHE15
BHIS18
BILE21
BHIS25
BVAL33
BASN34
BCYS35
BCYS38
BHIS39
BTHR59
BILE193
BLEU194
BPHE228
BPRO233
BHIS234
BARG239
BPHE274
BARG276
BARG282
BHOH831
BHEC1001
BHEC1003
BHOH1076

site_idBC9
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
BLYS29
BHIS30
BHIS37
BALA65
BCYS66
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH525
BHOH603
BHOH629
BHEC1002
BHEC1005
BHOH1084
BHOH1112

site_idCC1
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
BHOH526
BHOH528
BHOH637
BHOH833
BHOH857
BHEC1002
BHOH1076

site_idCC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NO2 B 1
ChainResidue
BPHE109
BARG131
BTYR303
BHIS361
BHEC1004
BHOH1089

site_idCC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 2
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH971
BHOH972

site_idCC4
Number of Residues8
DetailsBINDING SITE FOR RESIDUE MRD B 3
ChainResidue
BARG87
BGLN138
BPHE139
BTRP142
BVAL145
BTYR433
BARG497
BHOH653

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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