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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
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
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
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
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 site: {"description":"axial binding residue","evidences":[{"source":"PDB","id":"1GU6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RDZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RF7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3L1T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TOR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI2
Number of Residues32
DetailsBinding site: {"description":"covalent","evidences":[{"source":"PDB","id":"1GU6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RDZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RF7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3L1T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TOR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI3
Number of Residues8
DetailsBinding site: {"evidences":[{"source":"PDB","id":"1GU6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RDZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RF7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3L1T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TOR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI4
Number of Residues8
DetailsBinding site: {"evidences":[{"evidenceCode":"ECO:0000305"}]}
ChainResidueDetails

site_idSWS_FT_FI5
Number of Residues4
DetailsBinding site: {"evidences":[{"source":"PDB","id":"1GU6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RDZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3L1T","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3TOR","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

site_idSWS_FT_FI6
Number of Residues8
DetailsBinding site: {"description":"covalent","evidences":[{"source":"PDB","id":"1GU6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RDZ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2RF7","evidenceCode":"ECO:0007744"}]}
ChainResidueDetails

242500

PDB entries from 2025-10-01

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