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2FRV

CRYSTAL STRUCTURE OF THE OXIDIZED FORM OF NI-FE HYDROGENASE

Functional Information from GO Data
ChainGOidnamespacecontents
A0008901molecular_functionferredoxin hydrogenase activity
A0009055molecular_functionelectron transfer activity
A0009061biological_processanaerobic respiration
A0009375cellular_componentferredoxin hydrogenase complex
A0016020cellular_componentmembrane
A0016491molecular_functionoxidoreductase activity
A0042597cellular_componentperiplasmic space
A0044569cellular_component[Ni-Fe] hydrogenase complex
A0046872molecular_functionmetal ion binding
A0047806molecular_functioncytochrome-c3 hydrogenase activity
A0051536molecular_functioniron-sulfur cluster binding
A0051538molecular_function3 iron, 4 sulfur cluster binding
A0051539molecular_function4 iron, 4 sulfur cluster binding
B0008901molecular_functionferredoxin hydrogenase activity
B0016151molecular_functionnickel cation binding
B0016491molecular_functionoxidoreductase activity
B0042597cellular_componentperiplasmic space
B0046872molecular_functionmetal ion binding
B0047806molecular_functioncytochrome-c3 hydrogenase activity
C0008901molecular_functionferredoxin hydrogenase activity
C0009055molecular_functionelectron transfer activity
C0009061biological_processanaerobic respiration
C0009375cellular_componentferredoxin hydrogenase complex
C0016020cellular_componentmembrane
C0016491molecular_functionoxidoreductase activity
C0042597cellular_componentperiplasmic space
C0044569cellular_component[Ni-Fe] hydrogenase complex
C0046872molecular_functionmetal ion binding
C0047806molecular_functioncytochrome-c3 hydrogenase activity
C0051536molecular_functioniron-sulfur cluster binding
C0051538molecular_function3 iron, 4 sulfur cluster binding
C0051539molecular_function4 iron, 4 sulfur cluster binding
D0008901molecular_functionferredoxin hydrogenase activity
D0016151molecular_functionnickel cation binding
D0016491molecular_functionoxidoreductase activity
D0042597cellular_componentperiplasmic space
D0046872molecular_functionmetal ion binding
D0047806molecular_functioncytochrome-c3 hydrogenase activity
E0008901molecular_functionferredoxin hydrogenase activity
E0009055molecular_functionelectron transfer activity
E0009061biological_processanaerobic respiration
E0009375cellular_componentferredoxin hydrogenase complex
E0016020cellular_componentmembrane
E0016491molecular_functionoxidoreductase activity
E0042597cellular_componentperiplasmic space
E0044569cellular_component[Ni-Fe] hydrogenase complex
E0046872molecular_functionmetal ion binding
E0047806molecular_functioncytochrome-c3 hydrogenase activity
E0051536molecular_functioniron-sulfur cluster binding
E0051538molecular_function3 iron, 4 sulfur cluster binding
E0051539molecular_function4 iron, 4 sulfur cluster binding
F0008901molecular_functionferredoxin hydrogenase activity
F0016151molecular_functionnickel cation binding
F0016491molecular_functionoxidoreductase activity
F0042597cellular_componentperiplasmic space
F0046872molecular_functionmetal ion binding
F0047806molecular_functioncytochrome-c3 hydrogenase activity
G0008901molecular_functionferredoxin hydrogenase activity
G0009055molecular_functionelectron transfer activity
G0009061biological_processanaerobic respiration
G0009375cellular_componentferredoxin hydrogenase complex
G0016020cellular_componentmembrane
G0016491molecular_functionoxidoreductase activity
G0042597cellular_componentperiplasmic space
G0044569cellular_component[Ni-Fe] hydrogenase complex
G0046872molecular_functionmetal ion binding
G0047806molecular_functioncytochrome-c3 hydrogenase activity
G0051536molecular_functioniron-sulfur cluster binding
G0051538molecular_function3 iron, 4 sulfur cluster binding
G0051539molecular_function4 iron, 4 sulfur cluster binding
H0008901molecular_functionferredoxin hydrogenase activity
H0016151molecular_functionnickel cation binding
H0016491molecular_functionoxidoreductase activity
H0042597cellular_componentperiplasmic space
H0046872molecular_functionmetal ion binding
H0047806molecular_functioncytochrome-c3 hydrogenase activity
I0008901molecular_functionferredoxin hydrogenase activity
I0009055molecular_functionelectron transfer activity
I0009061biological_processanaerobic respiration
I0009375cellular_componentferredoxin hydrogenase complex
I0016020cellular_componentmembrane
I0016491molecular_functionoxidoreductase activity
I0042597cellular_componentperiplasmic space
I0044569cellular_component[Ni-Fe] hydrogenase complex
I0046872molecular_functionmetal ion binding
I0047806molecular_functioncytochrome-c3 hydrogenase activity
I0051536molecular_functioniron-sulfur cluster binding
I0051538molecular_function3 iron, 4 sulfur cluster binding
I0051539molecular_function4 iron, 4 sulfur cluster binding
J0008901molecular_functionferredoxin hydrogenase activity
J0016151molecular_functionnickel cation binding
J0016491molecular_functionoxidoreductase activity
J0042597cellular_componentperiplasmic space
J0046872molecular_functionmetal ion binding
J0047806molecular_functioncytochrome-c3 hydrogenase activity
L0008901molecular_functionferredoxin hydrogenase activity
L0016151molecular_functionnickel cation binding
L0016491molecular_functionoxidoreductase activity
L0042597cellular_componentperiplasmic space
L0046872molecular_functionmetal ion binding
L0047806molecular_functioncytochrome-c3 hydrogenase activity
S0008901molecular_functionferredoxin hydrogenase activity
S0009055molecular_functionelectron transfer activity
S0009061biological_processanaerobic respiration
S0009375cellular_componentferredoxin hydrogenase complex
S0016020cellular_componentmembrane
S0016491molecular_functionoxidoreductase activity
S0042597cellular_componentperiplasmic space
S0044569cellular_component[Ni-Fe] hydrogenase complex
S0046872molecular_functionmetal ion binding
S0047806molecular_functioncytochrome-c3 hydrogenase activity
S0051536molecular_functioniron-sulfur cluster binding
S0051538molecular_function3 iron, 4 sulfur cluster binding
S0051539molecular_function4 iron, 4 sulfur cluster binding
Functional Information from PDB Data
site_idAC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI L 538
ChainResidue
LCYS530
LCYS533
LFCO537
LO539
LCYS65
LCYS68

site_idAC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI B 538
ChainResidue
BCYS65
BCYS68
BCYS530
BCYS533
BFCO537
BO539

site_idAC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI D 538
ChainResidue
DCYS65
DCYS68
DCYS530
DCYS533
DFCO537
DO539

site_idAC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI F 538
ChainResidue
FCYS65
FCYS68
FCYS530
FCYS533
FFCO537
FO539

site_idAC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI H 538
ChainResidue
HCYS65
HCYS68
HCYS530
HCYS533
HFCO537
HO539

site_idAC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE NI J 538
ChainResidue
JCYS65
JCYS68
JCYS530
JCYS533
JFCO537
JO539

site_idAC7
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG L 540
ChainResidue
LGLU46
LLEU482
LHIS536
LHOH5011
LHOH5012
LHOH5013

site_idAC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG B 540
ChainResidue
BGLU46
BLEU482
BHIS536
BHOH5024
BHOH5025
BHOH5026

site_idAC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG D 540
ChainResidue
DGLU46
DLEU482
DHIS536
DHOH5037
DHOH5038
DHOH5039

site_idACT
Number of Residues7
DetailsNI-FE ACTIVE SITE.
ChainResidue
LCYS65
LCYS68
LCYS530
LCYS533
LFCO537
LNI538
LO539

site_idBC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG F 540
ChainResidue
FGLU46
FLEU482
FHIS536
FHOH5050
FHOH5051
FHOH5052

site_idBC2
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG H 540
ChainResidue
HGLU46
HLEU482
HHIS536
HHOH5063
HHOH5064
HHOH5065

site_idBC3
Number of Residues6
DetailsBINDING SITE FOR RESIDUE MG J 540
ChainResidue
JGLU46
JLEU482
JHIS536
JHOH5076
JHOH5077
JHOH5078

site_idBC4
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SF4 S 265
ChainResidue
SHIS185
SCYS188
SCYS213
SLEU214
SCYS219

site_idBC5
Number of Residues11
DetailsBINDING SITE FOR RESIDUE F3S S 266
ChainResidue
LLYS216
LGLN221
STHR224
SASN226
SCYS228
SPHE233
STRP238
SPRO239
SCYS246
SILE247
SCYS249

site_idBC6
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 S 267
ChainResidue
SCYS20
SGLY110
STHR111
SCYS112
SGLY147
SCYS148
SPRO149
LARG63
LHIS219
SGLU16
SCYS17

site_idBC7
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO L 537
ChainResidue
LCYS68
LVAL71
LHIS72
LALA461
LPRO462
LARG463
LLEU466
LVAL484
LPRO485
LSER486
LCYS533
LNI538
LO539

site_idBC8
Number of Residues6
DetailsBINDING SITE FOR RESIDUE O L 539
ChainResidue
LCYS68
LARG463
LCYS530
LCYS533
LFCO537
LNI538

site_idBC9
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SF4 A 265
ChainResidue
AHIS185
ACYS188
ACYS213
ALEU214
ACYS219

site_idCC1
Number of Residues11
DetailsBINDING SITE FOR RESIDUE F3S A 266
ChainResidue
ATHR224
AASN226
ACYS228
APHE233
ATRP238
APRO239
ACYS246
AILE247
ACYS249
BLYS216
BGLN221

site_idCC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 A 267
ChainResidue
AGLU16
ACYS17
ACYS20
AGLY110
ATHR111
ACYS112
AGLY147
ACYS148
APRO149
BARG63
BHIS219

site_idCC3
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO B 537
ChainResidue
BCYS68
BVAL71
BHIS72
BALA461
BPRO462
BARG463
BLEU466
BVAL484
BPRO485
BSER486
BCYS533
BNI538
BO539

site_idCC4
Number of Residues6
DetailsBINDING SITE FOR RESIDUE O B 539
ChainResidue
BCYS68
BARG463
BCYS530
BCYS533
BFCO537
BNI538

site_idCC5
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SF4 C 265
ChainResidue
CHIS185
CCYS188
CCYS213
CLEU214
CCYS219

site_idCC6
Number of Residues11
DetailsBINDING SITE FOR RESIDUE F3S C 266
ChainResidue
CTHR224
CASN226
CCYS228
CPHE233
CTRP238
CPRO239
CCYS246
CILE247
CCYS249
DLYS216
DGLN221

site_idCC7
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 C 267
ChainResidue
CGLU16
CCYS17
CCYS20
CGLY110
CTHR111
CCYS112
CGLY147
CCYS148
CPRO149
DARG63
DHIS219

site_idCC8
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO D 537
ChainResidue
DCYS68
DVAL71
DHIS72
DALA461
DPRO462
DARG463
DLEU466
DVAL484
DPRO485
DSER486
DCYS533
DNI538
DO539

site_idCC9
Number of Residues6
DetailsBINDING SITE FOR RESIDUE O D 539
ChainResidue
DCYS68
DARG463
DCYS530
DCYS533
DFCO537
DNI538

site_idDC1
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SF4 E 265
ChainResidue
EHIS185
ECYS188
ECYS213
ELEU214
ECYS219

site_idDC2
Number of Residues11
DetailsBINDING SITE FOR RESIDUE F3S E 266
ChainResidue
ETHR224
EASN226
ECYS228
EPHE233
ETRP238
EPRO239
ECYS246
EILE247
ECYS249
FLYS216
FGLN221

site_idDC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 E 267
ChainResidue
EGLU16
ECYS17
ECYS20
EGLY110
ETHR111
ECYS112
EGLY147
ECYS148
EPRO149
FARG63
FHIS219

site_idDC4
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO F 537
ChainResidue
FCYS68
FVAL71
FHIS72
FALA461
FPRO462
FARG463
FLEU466
FVAL484
FPRO485
FSER486
FCYS533
FNI538
FO539

site_idDC5
Number of Residues6
DetailsBINDING SITE FOR RESIDUE O F 539
ChainResidue
FCYS68
FARG463
FCYS530
FCYS533
FFCO537
FNI538

site_idDC6
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SF4 G 265
ChainResidue
GHIS185
GCYS188
GCYS213
GLEU214
GCYS219

site_idDC7
Number of Residues11
DetailsBINDING SITE FOR RESIDUE F3S G 266
ChainResidue
GTHR224
GASN226
GCYS228
GPHE233
GTRP238
GPRO239
GCYS246
GILE247
GCYS249
HLYS216
HGLN221

site_idDC8
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 G 267
ChainResidue
GGLU16
GCYS17
GCYS20
GGLY110
GTHR111
GCYS112
GGLY147
GCYS148
GPRO149
HARG63
HHIS219

site_idDC9
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO H 537
ChainResidue
HCYS68
HVAL71
HHIS72
HALA461
HPRO462
HARG463
HLEU466
HVAL484
HPRO485
HSER486
HCYS533
HNI538
HO539

site_idEC1
Number of Residues6
DetailsBINDING SITE FOR RESIDUE O H 539
ChainResidue
HCYS68
HARG463
HCYS530
HCYS533
HFCO537
HNI538

site_idEC2
Number of Residues5
DetailsBINDING SITE FOR RESIDUE SF4 I 265
ChainResidue
IHIS185
ICYS188
ICYS213
ILEU214
ICYS219

site_idEC3
Number of Residues11
DetailsBINDING SITE FOR RESIDUE F3S I 266
ChainResidue
ITHR224
IASN226
ICYS228
IPHE233
ITRP238
IPRO239
ICYS246
IILE247
ICYS249
JLYS216
JGLN221

site_idEC4
Number of Residues11
DetailsBINDING SITE FOR RESIDUE SF4 I 267
ChainResidue
IGLU16
ICYS17
ICYS20
IGLY110
ITHR111
ICYS112
IGLY147
ICYS148
IPRO149
JARG63
JHIS219

site_idEC5
Number of Residues13
DetailsBINDING SITE FOR RESIDUE FCO J 537
ChainResidue
JCYS68
JVAL71
JHIS72
JALA461
JPRO462
JARG463
JLEU466
JVAL484
JPRO485
JSER486
JCYS533
JNI538
JO539

site_idEC6
Number of Residues6
DetailsBINDING SITE FOR RESIDUE O J 539
ChainResidue
JCYS68
JARG463
JCYS530
JCYS533
JFCO537
JNI538

Functional Information from PROSITE/UniProt
site_idPS00507
Number of Residues26
DetailsNI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEmilkgrdprdaqhftQRaCGVC
ChainResidueDetails
LARG43-CYS68

site_idPS00508
Number of Residues10
DetailsNI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. YDPCIACgv.H
ChainResidueDetails
LTYR527-HIS536

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues12
DetailsBINDING: BINDING => ECO:0000269|PubMed:7854413
ChainResidueDetails
LGLY66
HILE531
JGLY66
JILE531
ACYS20
ACYS112
ACYS148
AHIS185
ACYS188
ACYS213
ACYS219
LILE531
ACYS228
ACYS246
ACYS249
CCYS17
CCYS20
CCYS112
CCYS148
CHIS185
CCYS188
CCYS213
BGLY66
CCYS219
CCYS228
CCYS246
CCYS249
ECYS17
ECYS20
ECYS112
ECYS148
EHIS185
ECYS188
BILE531
ECYS213
ECYS219
ECYS228
ECYS246
ECYS249
GCYS17
GCYS20
GCYS112
GCYS148
GHIS185
DGLY66
GCYS188
GCYS213
GCYS219
GCYS228
GCYS246
GCYS249
ICYS17
ICYS20
ICYS112
ICYS148
DILE531
IHIS185
ICYS188
ICYS213
ICYS219
ICYS228
ICYS246
ICYS249
FGLY66
FILE531
HGLY66

site_idSWS_FT_FI2
Number of Residues12
DetailsBINDING:
ChainResidueDetails
LTHR69
HGLY534
JTHR69
JGLY534
LGLY534
BTHR69
BGLY534
DTHR69
DGLY534
FTHR69
FGLY534
HTHR69

Catalytic Information from CSA
site_idCSA1
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
STHR18
LCYS530
LGLU18

site_idCSA10
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
FCYS530

site_idCSA11
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
HCYS530

site_idCSA12
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
JCYS530

site_idCSA2
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
ATHR18
BCYS530
BGLU18

site_idCSA3
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
CTHR18
DCYS530
DGLU18

site_idCSA4
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
FCYS530
FGLU18
ETHR18

site_idCSA5
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
HCYS530
HGLU18
GTHR18

site_idCSA6
Number of Residues3
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
JCYS530
JGLU18
ITHR18

site_idCSA7
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
LCYS530

site_idCSA8
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
BCYS530

site_idCSA9
Number of Residues1
DetailsAnnotated By Reference To The Literature 1cc1
ChainResidueDetails
DCYS530

site_idMCSA1
Number of Residues8
DetailsM-CSA 126
ChainResidueDetails
LGLY19hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
LGLY66activator, metal ligand
LTHR69activator, electrostatic stabiliser, metal ligand
LALA73electrostatic stabiliser, hydrogen bond donor
LGLY464electrostatic stabiliser, hydrogen bond donor
LTHR487electrostatic stabiliser, hydrogen bond donor
LILE531hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
LGLY534activator, electrostatic stabiliser, metal ligand

site_idMCSA2
Number of Residues8
DetailsM-CSA 126
ChainResidueDetails
BGLY19hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
BGLY66activator, metal ligand
BTHR69activator, electrostatic stabiliser, metal ligand
BALA73electrostatic stabiliser, hydrogen bond donor
BGLY464electrostatic stabiliser, hydrogen bond donor
BTHR487electrostatic stabiliser, hydrogen bond donor
BILE531hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
BGLY534activator, electrostatic stabiliser, metal ligand

site_idMCSA3
Number of Residues8
DetailsM-CSA 126
ChainResidueDetails
DGLY19hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
DGLY66activator, metal ligand
DTHR69activator, electrostatic stabiliser, metal ligand
DALA73electrostatic stabiliser, hydrogen bond donor
DGLY464electrostatic stabiliser, hydrogen bond donor
DTHR487electrostatic stabiliser, hydrogen bond donor
DILE531hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
DGLY534activator, electrostatic stabiliser, metal ligand

site_idMCSA4
Number of Residues8
DetailsM-CSA 126
ChainResidueDetails
FGLY19hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
FGLY66activator, metal ligand
FTHR69activator, electrostatic stabiliser, metal ligand
FALA73electrostatic stabiliser, hydrogen bond donor
FGLY464electrostatic stabiliser, hydrogen bond donor
FTHR487electrostatic stabiliser, hydrogen bond donor
FILE531hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
FGLY534activator, electrostatic stabiliser, metal ligand

site_idMCSA5
Number of Residues8
DetailsM-CSA 126
ChainResidueDetails
HGLY19hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
HGLY66activator, metal ligand
HTHR69activator, electrostatic stabiliser, metal ligand
HALA73electrostatic stabiliser, hydrogen bond donor
HGLY464electrostatic stabiliser, hydrogen bond donor
HTHR487electrostatic stabiliser, hydrogen bond donor
HILE531hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
HGLY534activator, electrostatic stabiliser, metal ligand

site_idMCSA6
Number of Residues8
DetailsM-CSA 126
ChainResidueDetails
JGLY19hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor, proton relay
JGLY66activator, metal ligand
JTHR69activator, electrostatic stabiliser, metal ligand
JALA73electrostatic stabiliser, hydrogen bond donor
JGLY464electrostatic stabiliser, hydrogen bond donor
JTHR487electrostatic stabiliser, hydrogen bond donor
JILE531hydrogen bond acceptor, hydrogen bond donor, metal ligand, proton acceptor, proton donor
JGLY534activator, electrostatic stabiliser, metal ligand

227561

PDB entries from 2024-11-20

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