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3F29

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

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
AHIS113
AARG242
ACYS299
AHIS300
ATYR303
ACYS305
AHIS361
AASN486
ASO3526
AHOH536
AHOH553
AALA114
AHOH672
AHOH673
AHOH679
AHOH688
AHEC1006
AASP125
AHIS126
AVAL129
AARG131
ACYS184
ACYS187
ALYS188

site_idAC2
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
AHIS70
AGLN73
ALEU225
AASN226
ACYS227
ACYS230
AHIS231
AMET384
ATYR395
ATHR396
AHIS398
AHOH646
AHOH755
AHOH776
AHOH939
AHOH973
AHEC1003
AHEC1006
AHOH1024

site_idAC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 1006
ChainResidue
ASER84
APRO116
AARG117
AHIS119
APHE121
AMET122
AASP125
ACYS187
ALYS188
AMET229
ACYS296
ACYS299
AHIS300
AHIS383
AMET384
ACA528
AHOH544
AHOH560
AHOH667
AHEC1004
AHEC1005
AHEC1007

site_idAC4
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
AHIS300
AGLU363
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
ACA528
AHOH667
AHOH668
AHOH676
AHOH680
AHOH867
AHOH921
AHEC1006

site_idAC5
Number of Residues15
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
APHE490
AHOH621
AHOH953
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418
AILE427

site_idAC6
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ACYS14
APHE15
AHIS18
AILE21
AHIS25
AVAL33
AASN34
ACYS35
ACYS38
AHIS39
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH613
AHOH877
AHOH996
AHEC1001
AHEC1003

site_idAC7
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ATHR68
ACYS69
AHIS70
ACYS227
AHIS231
AALA236
AHOH805
AHOH841
AHOH924
AHOH925
AHEC1002
AHEC1005
AHOH1063
AHOH1076
BTHR68

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
AHOH616
AHOH644
AHOH880
AHOH997
AHEC1002

site_idAC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SO3 A 526
ChainResidue
APHE109
AARG131
ATYR303
AHIS361
AHOH536
AHOH679
AHOH688
AHOH984
AHEC1004

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 527
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH758
AHOH759

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 528
ChainResidue
APRO116
AHOH574
AHOH867
AHOH946
AHEC1006
AHEC1007

site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG6 A 529
ChainResidue
ALEU311
AGLY314
AARG348
AALA355

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 A 530
ChainResidue
AASP428
ALYS431
AASN432
AHIS435
AHOH1031

site_idBC5
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG4 A 531
ChainResidue
AGLN138
APHE139
ATRP142

site_idBC6
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 A 532
ChainResidue
AARG171
APHE172
ALEU173
ASER174

site_idBC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 A 534
ChainResidue
AARG60
AASP62

site_idBC8
Number of Residues1
DetailsBINDING SITE FOR RESIDUE PG4 A 535
ChainResidue
AARG153

site_idBC9
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 1004
ChainResidue
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BTYR303
BCYS305
BHIS361
BASN486
BSO3526
BHOH537
BHOH668
BHOH783
BHOH784
BHOH790
BHEC1006

site_idCC1
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BHIS70
BGLN73
BLEU225
BASN226
BCYS227
BCYS230
BHIS231
BMET384
BTYR395
BTHR396
BHIS398
BHOH757
BHOH866
BHOH887
BHEC1003
BHEC1006
BHOH1056

site_idCC2
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1006
ChainResidue
BSER84
BPRO116
BARG117
BHIS119
BPHE121
BMET122
BASP125
BCYS187
BLYS188
BMET229
BCYS296
BCYS299
BHIS300
BHIS383
BMET384
BCA528
BHOH659
BHOH675
BHOH778
BHEC1004
BHEC1005
BHEC1007

site_idCC3
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BHIS300
BGLU363
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BARG404
BLYS431
BASN486
BPHE490
BHIS491
BCA528
BHOH778
BHOH779
BHOH787
BHOH791
BHOH976
BHEC1006
BHOH1038

site_idCC4
Number of Residues16
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BPHE490
BHOH564
BHOH611
BHOH1070

site_idCC5
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
BHOH726
BHOH986
BHEC1001
BHEC1003

site_idCC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
AHIS37
ATHR68
BLYS29
BHIS30
BHIS37
BALA65
BCYS66
BTHR68
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH551
BHOH643
BHOH654
BHOH916
BHOH950
BHEC1002
BHEC1005
BHOH1041
BHOH1042

site_idCC7
Number of Residues27
DetailsBINDING SITE FOR RESIDUE HEC B 1001
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BHIS44
BVAL45
BALA48
BSER49
BSER50
BARG51
BARG51
BARG52
BMET53
BARG56
BPRO57
BTHR59
BGLN275
BARG276
BHOH567
BHOH583
BHOH729
BHOH755
BHOH986
BHEC1002
BHOH1015
BHOH1085

site_idCC8
Number of Residues9
DetailsBINDING SITE FOR RESIDUE SO3 B 526
ChainResidue
BPHE109
BARG131
BTYR303
BGLN360
BHIS361
BHOH537
BHOH790
BHOH799
BHEC1004

site_idCC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 527
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH869
BHOH870

site_idDC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 528
ChainResidue
BPRO116
BHOH688
BHOH976
BHEC1006
BHEC1007
BHOH1063

site_idDC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO3 B 529
ChainResidue
BSER50
BSER50
BSER50
BHOH641
BHOH641
BHOH641

site_idDC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE PG6 B 530
ChainResidue
BLEU311
BGLY314
BARG348

site_idDC4
Number of Residues1
DetailsBINDING SITE FOR RESIDUE PG6 B 531
ChainResidue
BHIS435

site_idDC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE PG4 B 532
ChainResidue
BGLN138
BPHE139
BTRP142
BHOH578
BHOH636

site_idDC6
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 533
ChainResidue
BARG171
BPHE172

site_idDC7
Number of Residues2
DetailsBINDING SITE FOR RESIDUE PG4 B 535
ChainResidue
BARG60
BASP62

site_idDC8
Number of Residues4
DetailsBINDING SITE FOR RESIDUE PG4 B 536
ChainResidue
BPRO307
BGLY308
BTYR309
BARG316

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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