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2RDZ

High Resolution Crystal Structure of the Escherichia coli Cytochrome c Nitrite Reductase.

Functional Information from GO Data
ChainGOidnamespacecontents
A0005506molecular_functioniron ion binding
A0005509molecular_functioncalcium ion binding
A0006807biological_processobsolete nitrogen compound metabolic process
A0009061biological_processanaerobic respiration
A0016491molecular_functionoxidoreductase activity
A0016966molecular_functionnitric oxide reductase 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
B0005506molecular_functioniron ion binding
B0005509molecular_functioncalcium ion binding
B0006807biological_processobsolete nitrogen compound metabolic process
B0009061biological_processanaerobic respiration
B0016491molecular_functionoxidoreductase activity
B0016966molecular_functionnitric oxide reductase 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
C0005506molecular_functioniron ion binding
C0005509molecular_functioncalcium ion binding
C0006807biological_processobsolete nitrogen compound metabolic process
C0009061biological_processanaerobic respiration
C0016491molecular_functionoxidoreductase activity
C0016966molecular_functionnitric oxide reductase activity
C0019645biological_processanaerobic electron transport chain
C0020037molecular_functionheme binding
C0030288cellular_componentouter membrane-bounded periplasmic space
C0042128biological_processnitrate assimilation
C0042279molecular_functionnitrite reductase (cytochrome, ammonia-forming) activity
C0042597cellular_componentperiplasmic space
C0046872molecular_functionmetal ion binding
D0005506molecular_functioniron ion binding
D0005509molecular_functioncalcium ion binding
D0006807biological_processobsolete nitrogen compound metabolic process
D0009061biological_processanaerobic respiration
D0016491molecular_functionoxidoreductase activity
D0016966molecular_functionnitric oxide reductase activity
D0019645biological_processanaerobic electron transport chain
D0020037molecular_functionheme binding
D0030288cellular_componentouter membrane-bounded periplasmic space
D0042128biological_processnitrate assimilation
D0042279molecular_functionnitrite reductase (cytochrome, ammonia-forming) activity
D0042597cellular_componentperiplasmic space
D0046872molecular_functionmetal ion binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA A1501
ChainResidue
AGLU215
ATYR216
ALYS261
AGLN263
AHOH489
AHOH499

site_idAC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE CA A1502
ChainResidue
AHOH623
AHOH650
AHOH908
AHOH936
AHEC3
AHEC4
APRO91

site_idAC3
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC A 1
ChainResidue
AHEC3
ATYR88
AASN89
AASP100
ATHR104
AARG106
ACYS122
ACYS125
ALYS126
ACYS212
AHIS213
ATYR216
APHE218
AHIS264
AHIS388
AHOH483
AHOH484
AHOH487
AHOH494
AHOH501
AHOH529
AHOH541
AHOH563

site_idAC4
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC A 2
ChainResidue
AHEC3
AHIS49
AGLN52
ATYR53
ATRP56
AGLY159
ACYS160
ACYS163
AHIS164
APHE171
AGLY174
AARG201
AGLN205
AILE283
ALYS289
ATYR298
ATHR299
AHIS301
AHOH552
AHOH576

site_idAC5
Number of Residues26
DetailsBINDING SITE FOR RESIDUE HEC A 3
ChainResidue
AHEC1
AHEC2
AHEC4
AGLN62
APRO91
AARG92
AGLY93
AHIS94
APHE96
AALA97
AASP100
ACYS125
ALYS126
ALEU158
AVAL208
ACYS209
ACYS212
AHIS213
AILE283
AHIS286
AMET287
AILE303
AHOH498
AHOH623
AHOH747
ACA1502

site_idAC6
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC A 4
ChainResidue
AMET392
AHIS393
AHOH606
AHOH650
AHOH731
AHOH787
AHOH873
ACA1502
AHEC3
AHEC5
AHIS213
AGLU266
ATRP270
AHIS275
AVAL280
ATHR281
ACYS282
ACYS285
AHIS286
AASN305
APRO306
APHE307
AVAL329
AHIS388
AHIS391

site_idAC7
Number of Residues17
DetailsBINDING SITE FOR RESIDUE HEC A 5
ChainResidue
AHEC4
AEDO11
AILE274
AHIS275
AASN278
APHE307
ATHR313
ACYS314
ACYS317
AHIS318
AARG332
AMET392
AHOH503
AHOH525
BHEC5
BHIS318
BGLN320

site_idAC8
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 A2001
ChainResidue
APHE307
AASP308
AASN309
APHE310
AALA311
ALYS322
AHOH815
AHOH981

site_idAC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 481
ChainResidue
AMET233
ALYS234
AVAL235
AGLU397
AMET401
AHOH523
AHOH950

site_idBC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 11
ChainResidue
AHEC5
AILE274
AARG332
AGLU396
AHOH525
BHEC5
BARG332

site_idBC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 13
ChainResidue
AASP72
AASN337
ALYS340
AILE341
AHOH943

site_idBC3
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 14
ChainResidue
AASN165
AGLU177
ALEU178
ATHR179

site_idBC4
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 15
ChainResidue
AHIS286
ALYS302
AGLY304
AASN305
AASN309
AHOH585
AHOH812

site_idBC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO A 20
ChainResidue
AASP411
ATHR414
ALYS415
AARG418
AHOH645
BARG413
BHOH580

site_idBC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE EDO A 21
ChainResidue
AGLY81
ATYR82
APRO83
AARG86
AHOH1025

site_idBC7
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO A 22
ChainResidue
AASP345
AVAL348
AILE431
AHOH635

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA B1501
ChainResidue
BGLU215
BTYR216
BLYS261
BGLN263
BHOH504
BHOH528

site_idBC9
Number of Residues7
DetailsBINDING SITE FOR RESIDUE CA B1502
ChainResidue
BHEC3
BHEC4
BPRO91
BHOH661
BHOH676
BHOH716
BHOH955

site_idCC1
Number of Residues27
DetailsBINDING SITE FOR RESIDUE HEC B 1
ChainResidue
BHEC3
BTYR88
BASN89
BPRO91
BASP100
BTHR104
BARG106
BTHR107
BLEU118
BCYS122
BCYS125
BLYS126
BCYS212
BHIS213
BTYR216
BVAL225
BHIS264
BHIS388
BHOH484
BHOH485
BHOH490
BHOH493
BHOH517
BHOH522
BHOH534
BHOH545
BHOH1025

site_idCC2
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC B 2
ChainResidue
BHEC3
BHIS49
BGLN52
BTYR53
BTRP56
BGLY159
BCYS160
BCYS163
BHIS164
BPHE171
BGLY174
BARG201
BGLN205
BILE283
BMET287
BLYS289
BTYR298
BTHR299
BHIS301
BHOH527
BHOH546

site_idCC3
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 3
ChainResidue
BHEC1
BHEC2
BHEC4
BGLN62
BPRO91
BARG92
BGLY93
BHIS94
BPHE96
BALA97
BASP100
BCYS125
BLEU158
BVAL208
BCYS209
BCYS212
BHIS213
BHIS286
BMET287
BILE303
BHOH661
BHOH720
BCA1502

site_idCC4
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC B 4
ChainResidue
BHEC3
BHEC5
BHIS213
BGLU266
BTRP270
BHIS275
BVAL280
BTHR281
BCYS282
BCYS285
BHIS286
BASN305
BPRO306
BPHE307
BVAL329
BHIS388
BHIS391
BMET392
BHIS393
BHOH676
BHOH686
BHOH692
BCA1502

site_idCC5
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC B 5
ChainResidue
AHEC5
AEDO11
AHIS318
AGLN320
BHEC4
BILE274
BHIS275
BVAL280
BPRO306
BPHE307
BTHR313
BCYS314
BCYS317
BHIS318
BARG332
BMET392
BHOH506
BHOH509
BHOH568
BHOH701

site_idCC6
Number of Residues8
DetailsBINDING SITE FOR RESIDUE SO4 B2001
ChainResidue
BPHE307
BASP308
BASN309
BPHE310
BALA311
BLYS322
BHOH804
BHOH917

site_idCC7
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 481
ChainResidue
BMET233
BLYS234
BVAL235
BGLU268
BGLU397
BMET401
BHOH558

site_idCC8
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 16
ChainResidue
AARG413
AHOH559
BASP411
BTHR414
BLYS415
BARG418
BHOH813

site_idCC9
Number of Residues3
DetailsBINDING SITE FOR RESIDUE EDO B 17
ChainResidue
BASP407
BLYS408
BASP411

site_idDC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 18
ChainResidue
BCYS285
BHIS286
BLYS302
BGLY304
BASN305
BPRO306
BHOH697

site_idDC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO B 19
ChainResidue
BMET120
BASP137
BGLY141
BTYR142
BHIS144
BARG149
BHOH499

site_idDC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO B 20
ChainResidue
BASP345
BVAL348
BILE434
BHOH643
BHOH934
BHOH954

site_idDC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA C1501
ChainResidue
CGLU215
CTYR216
CLYS261
CGLN263
CHOH495
CHOH514

site_idDC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA C1502
ChainResidue
CHEC3
CHEC4
CPRO91
CHOH609
CHOH712
CHOH769

site_idDC6
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC C 1
ChainResidue
CHEC3
CTYR88
CASN89
CASP100
CTHR104
CARG106
CLEU118
CCYS122
CCYS125
CLYS126
CCYS212
CHIS213
CTYR216
CPHE218
CVAL225
CHIS264
CHIS388
CHOH486
CHOH491
CHOH505
CHOH507
CHOH517
CHOH518
CHOH522
CHOH558

site_idDC7
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC C 2
ChainResidue
CHEC3
CHIS49
CGLN52
CTYR53
CTRP56
CGLY159
CCYS160
CCYS163
CHIS164
CPHE171
CGLY174
CPRO176
CARG201
CGLN205
CILE283
CLYS289
CTYR298
CTHR299
CHIS301
CHOH542
CHOH630

site_idDC8
Number of Residues23
DetailsBINDING SITE FOR RESIDUE HEC C 3
ChainResidue
CHEC1
CHEC2
CHEC4
CGLN62
CPRO91
CARG92
CGLY93
CHIS94
CPHE96
CALA97
CASP100
CCYS125
CLEU158
CVAL208
CCYS209
CCYS212
CHIS213
CHIS286
CMET287
CILE303
CHOH640
CHOH712
CCA1502

site_idDC9
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC C 4
ChainResidue
CHEC3
CHEC5
CHIS213
CGLU266
CTRP270
CHIS275
CVAL280
CTHR281
CCYS282
CCYS285
CHIS286
CASN305
CPRO306
CVAL329
CHIS388
CHIS391
CMET392
CHIS393
CHOH578
CHOH660
CHOH674
CHOH769
CHOH884
CHOH963
CCA1502

site_idEC1
Number of Residues18
DetailsBINDING SITE FOR RESIDUE HEC C 5
ChainResidue
CHEC4
CEDO12
CILE274
CHIS275
CVAL280
CASP284
CPHE307
CTHR313
CCYS314
CCYS317
CHIS318
CARG332
CMET392
CHOH493
CHOH500
DHEC5
DHIS318
DGLN320

site_idEC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 C2001
ChainResidue
CPHE307
CASP308
CASN309
CPHE310
CALA311
CLYS322

site_idEC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 481
ChainResidue
CMET233
CLYS234
CVAL235
CGLU268
CGLU397
CHOH508

site_idEC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 12
ChainResidue
CHEC5
CILE274
CARG332
DHEC5
DILE274
DARG332

site_idEC5
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO C 21
ChainResidue
CASP407
CLYS408
CASP411
CHOH889

site_idEC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 22
ChainResidue
CASP411
CLYS415
CARG418
CHOH681
DARG413
DHOH639

site_idEC7
Number of Residues8
DetailsBINDING SITE FOR RESIDUE EDO C 23
ChainResidue
CCYS285
CHIS286
CLYS302
CGLY304
CASN305
CPRO306
CASN309
CHOH759

site_idEC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO C 25
ChainResidue
CASP345
CILE431
CILE434
CHOH529
CHOH689
CHOH807

site_idEC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE CA D1501
ChainResidue
DGLU215
DTYR216
DLYS261
DGLN263
DHOH497
DHOH520

site_idFC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE CA D1502
ChainResidue
DHEC3
DHEC4
DPRO91
DHOH707
DHOH758

site_idFC2
Number of Residues26
DetailsBINDING SITE FOR RESIDUE HEC D 1
ChainResidue
DHEC3
DTYR88
DASN89
DPRO91
DASP100
DTHR104
DARG106
DLEU118
DCYS122
DCYS125
DLYS126
DCYS212
DHIS213
DTYR216
DVAL225
DHIS264
DHIS388
DHOH487
DHOH489
DHOH490
DHOH492
DHOH511
DHOH523
DHOH529
DHOH542
DHOH555

site_idFC3
Number of Residues21
DetailsBINDING SITE FOR RESIDUE HEC D 2
ChainResidue
DHEC3
DHIS49
DGLN52
DTYR53
DTRP56
DGLY159
DCYS160
DCYS163
DHIS164
DPHE171
DGLY174
DARG201
DGLN205
DILE283
DMET287
DLYS289
DTYR298
DTHR299
DHIS301
DHOH585
DHOH612

site_idFC4
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC D 3
ChainResidue
DHEC1
DHEC2
DHEC4
DGLN62
DPRO91
DARG92
DGLY93
DHIS94
DPHE96
DALA97
DASP100
DCYS125
DLYS126
DLEU158
DVAL208
DCYS209
DCYS212
DHIS213
DHIS286
DMET287
DILE303
DHOH522
DHOH707
DHOH776
DCA1502

site_idFC5
Number of Residues25
DetailsBINDING SITE FOR RESIDUE HEC D 4
ChainResidue
DHEC3
DHEC5
DHIS213
DGLU266
DTRP270
DHIS275
DVAL280
DTHR281
DCYS282
DCYS285
DHIS286
DASN305
DPRO306
DVAL329
DHIS391
DMET392
DHIS393
DHOH604
DHOH659
DHOH681
DHOH700
DHOH709
DHOH738
DHOH779
DCA1502

site_idFC6
Number of Residues20
DetailsBINDING SITE FOR RESIDUE HEC D 5
ChainResidue
CHEC5
CEDO12
CHIS318
CGLN320
DHEC4
DILE274
DHIS275
DVAL280
DPRO306
DPHE307
DTHR313
DCYS314
DCYS317
DHIS318
DARG332
DMET392
DHOH525
DHOH550
DHOH567
DHOH667

site_idFC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE SO4 D2001
ChainResidue
DPHE307
DASP308
DASN309
DPHE310
DALA311
DLYS322

site_idFC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO D 481
ChainResidue
DARG65
DASN89
DARG92
DASP100
DHOH614
DHOH1029

site_idFC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE EDO D 482
ChainResidue
CARG413
CHOH554
CHOH622
DTHR414
DLYS415
DARG418

site_idGC1
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 6
ChainResidue
DMET233
DLYS234
DVAL235
DGLU268
DGLU397
DHOH623
DHOH1011

site_idGC2
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 21
ChainResidue
DSER55
DTYR298
DASP300
DLYS302
DHOH689
DHOH928
DHOH995

site_idGC3
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 22
ChainResidue
DGLY81
DTYR82
DPRO83
DARG86
DLEU446
DHOH528
DHOH642

site_idGC4
Number of Residues4
DetailsBINDING SITE FOR RESIDUE EDO D 23
ChainResidue
DASP345
DVAL348
DHIS349
DHOH730

site_idGC5
Number of Residues7
DetailsBINDING SITE FOR RESIDUE EDO D 24
ChainResidue
DMET120
DASP137
DGLY141
DTYR142
DHIS144
DARG149
DHOH512

site_idGC6
Number of Residues9
DetailsBINDING SITE FOR RESIDUE EDO D 25
ChainResidue
ATHR436
AHOH753
CHOH646
DGLU236
DGLU239
DARG380
DHOH510
DHOH649
DHOH1035

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues36
DetailsBINDING: axial binding residue => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR
ChainResidueDetails
AHIS94
AHIS393
BHIS94
BLYS126
BHIS164
BHIS213
BHIS275
BHIS286
BHIS301
BHIS318
BHIS393
CHIS94
CLYS126
CHIS164
CHIS213
CHIS275
CHIS286
CHIS301
CHIS318
CHIS393
DHIS94
DLYS126
DHIS164
DHIS213
DHIS275
DHIS286
DHIS301
DHIS318
DHIS393
ALYS126
AHIS164
AHIS213
AHIS275
AHIS286
AHIS301
AHIS318

site_idSWS_FT_FI2
Number of Residues32
DetailsBINDING: covalent => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR
ChainResidueDetails
ACYS209
ACYS212
ACYS282
ACYS314
BCYS122
BCYS125
BCYS160
BCYS163
BCYS209
BCYS212
BCYS282
BCYS314
CCYS122
CCYS125
CCYS160
CCYS163
CCYS209
CCYS212
CCYS282
CCYS314
DCYS122
DCYS125
DCYS160
DCYS163
DCYS209
DCYS212
DCYS282
DCYS314
ACYS122
ACYS125
ACYS160
ACYS163

site_idSWS_FT_FI3
Number of Residues8
DetailsBINDING: BINDING => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR
ChainResidueDetails
AGLU215
ALYS261
BGLU215
BLYS261
CGLU215
CLYS261
DGLU215
DLYS261

site_idSWS_FT_FI4
Number of Residues8
DetailsBINDING: BINDING => ECO:0000305
ChainResidueDetails
CTYR216
CHIS264
DTYR216
DHIS264
ATYR216
AHIS264
BTYR216
BHIS264

site_idSWS_FT_FI5
Number of Residues4
DetailsBINDING: BINDING => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:3L1T, ECO:0007744|PDB:3TOR
ChainResidueDetails
AGLN263
BGLN263
CGLN263
DGLN263

site_idSWS_FT_FI6
Number of Residues8
DetailsBINDING: covalent => ECO:0007744|PDB:1GU6, ECO:0007744|PDB:2RDZ, ECO:0007744|PDB:2RF7
ChainResidueDetails
CCYS285
CCYS317
DCYS285
DCYS317
ACYS285
ACYS317
BCYS285
BCYS317

219869

PDB entries from 2024-05-15

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