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3GM6

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

Functional Information from GO Data
ChainGOidnamespacecontents
A0005509molecular_functioncalcium ion binding
A0016491molecular_functionoxidoreductase activity
A0019645biological_processanaerobic electron transport chain
A0020037molecular_functionheme binding
A0030288cellular_componentouter membrane-bounded periplasmic space
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
B0019645biological_processanaerobic electron transport chain
B0020037molecular_functionheme binding
B0030288cellular_componentouter membrane-bounded periplasmic space
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 Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1004
ChainResidue
AHIS113
AARG242
ACYS299
AHIS300
ATYR303
AHIS361
AASN486
APO4526
AHOH545
AHOH713
AHOH714
AALA114
AHOH720
AHEC1006
AASP125
AHIS126
AVAL129
AARG131
ACYS184
ACYS187
ALYS188

site_idAC2
Number of Residues14
DetailsBINDING SITE FOR RESIDUE HEC A 1005
ChainResidue
AHIS70
AGLN73
ALEU225
ACYS227
ACYS230
AHIS231
AMET384
ALYS386
ATYR395
ATHR396
AHIS398
AHOH818
AHOH846
AHEC1003

site_idAC3
Number of Residues23
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
AHOH534
AHOH551
AHOH553
AHOH708
AHEC1004
AHEC1007

site_idAC4
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC A 1007
ChainResidue
APHE367
AHIS372
AALA378
ACYS379
ACYS382
AHIS383
ATHR402
AARG404
ALYS431
AASN486
APHE490
AHIS491
AHOH551
AHOH708
AHOH709
AHOH710
AHOH717
AHOH721
AHEC1006

site_idAC5
Number of Residues13
DetailsBINDING SITE FOR RESIDUE HEC A 1008
ChainResidue
AASN141
ATRP142
AGLN143
AVAL371
AHIS372
APRO403
AALA410
ACYS411
ACYS414
AHIS415
ATRP418
AILE427
AHOH652

site_idAC6
Number of Residues22
DetailsBINDING SITE FOR RESIDUE HEC A 1002
ChainResidue
ALEU194
APHE228
APRO233
AHIS234
AARG239
APHE274
AARG276
AARG282
AHOH643
AHOH680
AHOH984
AHEC1001
AHEC1003
ACYS14
APHE15
AHIS18
AHIS25
AVAL33
AASN34
ACYS35
ACYS38
AHIS39

site_idAC7
Number of Residues15
DetailsBINDING SITE FOR RESIDUE HEC A 1003
ChainResidue
ALYS29
AHIS30
AHIS37
AALA65
ACYS66
ATHR68
ACYS69
AHIS70
AHIS231
AALA236
AHOH905
AHEC1002
AHEC1005
AHOH1030
AHOH1040

site_idAC8
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC A 1001
ChainResidue
AGLN13
ACYS14
ACYS17
AHIS18
AHIS39
AHIS44
AALA48
ASER49
ASER50
AARG52
AARG56
APRO57
ATHR59
ALEU194
AARG276
AGLY277
AHOH646
AHOH685
AHOH973
AHOH982
AHEC1002

site_idAC9
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PO4 A 526
ChainResidue
APHE109
AARG131
ATYR303
AGLN360
AHIS361
AHOH715
AHOH720
AHOH732
AHEC1004

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A 527
ChainResidue
AGLU302
ATYR303
ALYS358
AGLN360
AHOH821
AHOH822

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MPD A 528
ChainResidue
AARG87
AGLN138
APHE139
ATRP142
AARG497
AHOH910

site_idBC3
Number of Residues3
DetailsBINDING SITE FOR RESIDUE MPD A 529
ChainResidue
ALYS431
AASN432
AHIS435

site_idBC4
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 1004
ChainResidue
BHIS113
BALA114
BASP125
BHIS126
BVAL129
BARG131
BCYS184
BCYS187
BLYS188
BARG242
BCYS299
BHIS300
BTYR303
BHIS361
BASN486
BPO4526
BHOH620
BHOH766
BHOH767
BHOH773
BHEC1006

site_idBC5
Number of Residues15
DetailsBINDING SITE FOR RESIDUE HEC B 1005
ChainResidue
BHIS70
BGLN73
BLEU225
BCYS227
BCYS230
BHIS231
BMET384
BTYR395
BTHR396
BHIS398
BHOH583
BHOH871
BHOH899
BHEC1003
BHOH1053

site_idBC6
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
BHOH609
BHOH627
BHOH629
BHOH761
BHEC1004
BHEC1007

site_idBC7
Number of Residues19
DetailsBINDING SITE FOR RESIDUE HEC B 1007
ChainResidue
BPHE367
BHIS372
BALA378
BCYS379
BCYS382
BHIS383
BTHR402
BARG404
BLYS431
BASN486
BPHE490
BHIS491
BHOH627
BHOH761
BHOH762
BHOH763
BHOH770
BHOH774
BHEC1006

site_idBC8
Number of Residues13
DetailsBINDING SITE FOR RESIDUE HEC B 1008
ChainResidue
BASN141
BTRP142
BGLN143
BVAL371
BHIS372
BPRO403
BALA410
BCYS411
BCYS414
BHIS415
BTRP418
BILE427
BHOH555

site_idBC9
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
BHOH699
BHOH733
BHEC1001
BHEC1003

site_idCC1
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC B 1003
ChainResidue
ATHR68
BLYS29
BHIS30
BHIS37
BALA65
BCYS66
BCYS69
BHIS70
BCYS227
BHIS231
BALA236
BHOH534
BHOH573
BHOH598
BHOH959
BHEC1002
BHEC1005
BHOH1059

site_idCC2
Number of Residues27
DetailsBINDING SITE FOR RESIDUE HEC B 1001
ChainResidue
BGLN13
BCYS14
BCYS17
BHIS18
BHIS39
BHIS44
BVAL45
BALA48
BSER49
BARG51
BARG51
BARG52
BMET53
BARG56
BPRO57
BTHR59
BLEU194
BGLN275
BARG276
BHOH702
BHOH733
BHOH738
BHOH916
BHOH917
BHEC1002
BHOH1037
BHOH1046

site_idCC3
Number of Residues9
DetailsBINDING SITE FOR RESIDUE PO4 B 526
ChainResidue
BPHE109
BARG131
BTYR303
BGLN360
BHIS361
BHOH768
BHOH773
BHOH785
BHEC1004

site_idCC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B 527
ChainResidue
BGLU302
BTYR303
BLYS358
BGLN360
BHOH874
BHOH875

site_idCC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MPD B 528
ChainResidue
BARG87
BGLN138
BPHE139
BTRP142
BARG497
BHOH964

site_idCC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE MRD B 529
ChainResidue
BSER95
BLYS431
BHIS435
BHOH556
BHOH1065

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 2024-11-06

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