Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

4URH

High-resolution structure of partially oxidized D. fructosovorans NiFe-hydrogenase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0009055	molecular_function	electron transfer activity
A	0009061	biological_process	anaerobic respiration
A	0009375	cellular_component	ferredoxin hydrogenase complex
A	0016020	cellular_component	membrane
A	0016491	molecular_function	oxidoreductase activity
A	0042597	cellular_component	periplasmic space
A	0044569	cellular_component	[Ni-Fe] hydrogenase complex
A	0046872	molecular_function	metal ion binding
A	0047806	molecular_function	cytochrome-c3 hydrogenase activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051538	molecular_function	3 iron, 4 sulfur cluster binding
A	0051539	molecular_function	4 iron, 4 sulfur cluster binding
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0009055	molecular_function	electron transfer activity
B	0009061	biological_process	anaerobic respiration
B	0009375	cellular_component	ferredoxin hydrogenase complex
B	0016020	cellular_component	membrane
B	0016491	molecular_function	oxidoreductase activity
B	0042597	cellular_component	periplasmic space
B	0044569	cellular_component	[Ni-Fe] hydrogenase complex
B	0046872	molecular_function	metal ion binding
B	0047806	molecular_function	cytochrome-c3 hydrogenase activity
B	0051536	molecular_function	iron-sulfur cluster binding
B	0051538	molecular_function	3 iron, 4 sulfur cluster binding
B	0051539	molecular_function	4 iron, 4 sulfur cluster binding
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0009055	molecular_function	electron transfer activity
C	0009061	biological_process	anaerobic respiration
C	0009375	cellular_component	ferredoxin hydrogenase complex
C	0016020	cellular_component	membrane
C	0016491	molecular_function	oxidoreductase activity
C	0042597	cellular_component	periplasmic space
C	0044569	cellular_component	[Ni-Fe] hydrogenase complex
C	0046872	molecular_function	metal ion binding
C	0047806	molecular_function	cytochrome-c3 hydrogenase activity
C	0051536	molecular_function	iron-sulfur cluster binding
C	0051538	molecular_function	3 iron, 4 sulfur cluster binding
C	0051539	molecular_function	4 iron, 4 sulfur cluster binding
Q	0008901	molecular_function	ferredoxin hydrogenase activity
Q	0016151	molecular_function	nickel cation binding
Q	0016491	molecular_function	oxidoreductase activity
Q	0042597	cellular_component	periplasmic space
Q	0046872	molecular_function	metal ion binding
Q	0047806	molecular_function	cytochrome-c3 hydrogenase activity
R	0008901	molecular_function	ferredoxin hydrogenase activity
R	0016151	molecular_function	nickel cation binding
R	0016491	molecular_function	oxidoreductase activity
R	0042597	cellular_component	periplasmic space
R	0046872	molecular_function	metal ion binding
R	0047806	molecular_function	cytochrome-c3 hydrogenase activity
S	0008901	molecular_function	ferredoxin hydrogenase activity
S	0016151	molecular_function	nickel cation binding
S	0016491	molecular_function	oxidoreductase activity
S	0042597	cellular_component	periplasmic space
S	0046872	molecular_function	metal ion binding
S	0047806	molecular_function	cytochrome-c3 hydrogenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 A 1265

Chain	Residue
A	HIS184
A	CYS187
A	ARG189
A	LEU190
A	CYS212
A	LEU213
A	CYS218

site_id	AC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F3S A 1266

Chain	Residue
A	CYS227
A	PHE232
A	TRP237
A	CYS245
A	LEU246
A	CYS248
Q	GLN230
A	THR223
A	ASN225

site_id	AC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 A 1267

Chain	Residue
A	GLU16
A	CYS17
A	CYS20
A	THR113
A	CYS114
A	GLY146
A	CYS147
A	PRO148
Q	ARG70
Q	HIS228

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 1268

Chain	Residue
A	SER134
A	VAL139
A	LYS140
A	THR141
A	ASN172
A	GLY173
A	GOL1269
A	HOH2256

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL A 1269

Chain	Residue
A	LYS140
A	LEU169
A	ASP170
A	GOL1268

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 B 1265

Chain	Residue
B	HIS184
B	CYS187
B	ARG189
B	LEU190
B	CYS212
B	LEU213
B	CYS218

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F3S B 1266

Chain	Residue
B	ASN225
B	CYS227
B	PHE232
B	CYS245
B	LEU246
B	CYS248
R	LYS225
R	GLN230

site_id	AC8
Number of Residues	11
Details	BINDING SITE FOR RESIDUE SF4 B 1267

Chain	Residue
B	GLU16
B	CYS17
B	CYS20
B	GLY112
B	THR113
B	CYS114
B	GLY146
B	CYS147
B	PRO148
R	ARG70
R	HIS228

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SF4 C 1265

Chain	Residue
C	HIS184
C	CYS187
C	ARG189
C	LEU190
C	CYS212
C	LEU213
C	CYS218

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE F3S C 1266

Chain	Residue
C	THR223
C	ASN225
C	CYS227
C	PHE232
C	TRP237
C	CYS245
C	LEU246
C	CYS248
S	LYS225
S	GLN230

site_id	BC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE SF4 C 1267

Chain	Residue
C	GLU16
C	CYS17
C	CYS20
C	THR113
C	CYS114
C	GLY146
C	CYS147
C	PRO148
S	ARG70
S	HIS228

site_id	BC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO Q 1550

Chain	Residue
Q	PRO498
Q	SER499
Q	CYS546
Q	NI1551
Q	HOH2066
Q	CSX75
Q	VAL78
Q	HIS79
Q	ALA474
Q	PRO475
Q	ARG476
Q	LEU479
Q	VAL497

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI Q 1551

Chain	Residue
Q	CYS72
Q	CSX75
Q	CYS543
Q	CYS546
Q	FCO1550
Q	HOH2066

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG Q 1552

Chain	Residue
Q	GLU53
Q	LEU495
Q	HIS549
Q	HOH2047
Q	HOH2048
Q	HOH2279

site_id	BC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL Q 1553

Chain	Residue
Q	ARG100
Q	ASN104
Q	PHE295
Q	ALA296
Q	THR297
Q	TRP442
Q	GLU445
Q	HOH2105
Q	HOH2251
Q	HOH2389

site_id	BC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE MG Q 1554

Chain	Residue
A	HOH2082
A	HOH2083
C	HOH2168
C	HOH2172
C	HOH2186
Q	ASN181
Q	HOH2171

site_id	BC8
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO R 1550

Chain	Residue
R	CSX75
R	VAL78
R	HIS79
R	ALA474
R	PRO475
R	ARG476
R	LEU479
R	VAL497
R	PRO498
R	SER499
R	CYS546
R	NI1551
R	HOH2053

site_id	BC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI R 1551

Chain	Residue
R	CYS72
R	CSX75
R	CYS543
R	CYS546
R	FCO1550
R	HOH2053

site_id	CC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG R 1552

Chain	Residue
R	GLU53
R	LEU495
R	HIS549
R	HOH2039
R	HOH2040
R	HOH2203

site_id	CC2
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL R 1553

Chain	Residue
R	ARG100
R	ASN104
R	PHE295
R	ALA296
R	THR297
R	GLU445
R	HOH2069
R	HOH2179
R	HOH2303

site_id	CC3
Number of Residues	13
Details	BINDING SITE FOR RESIDUE FCO S 1550

Chain	Residue
S	CSX75
S	VAL78
S	HIS79
S	ALA474
S	PRO475
S	ARG476
S	LEU479
S	VAL497
S	PRO498
S	SER499
S	CYS546
S	NI1551
S	HOH2047

site_id	CC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE NI S 1551

Chain	Residue
S	CYS72
S	CSX75
S	CYS543
S	CYS546
S	FCO1550
S	HOH2047

site_id	CC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG S 1552

Chain	Residue
S	GLU53
S	LEU495
S	HIS549
S	HOH2031
S	HOH2032
S	HOH2193

site_id	CC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE GOL S 1553

Chain	Residue
S	ARG100
S	ASN104
S	PHE295
S	ALA296
S	THR297
S	TRP442
S	GLU445
S	HOH2073
S	HOH2171
S	HOH2281

Functional Information from PROSITE/UniProt

site_id	PS00507
Number of Residues	26
Details	NI_HGENASE_L_1 Nickel-dependent hydrogenases large subunit signature 1. RGLEiilkgrdprdaqhftQRaCGVC

Chain	Residue	Details
Q	ARG50-CSX75

site_id	PS00508
Number of Residues	10
Details	NI_HGENASE_L_2 Nickel-dependent hydrogenases large subunit signature 2. FDPCIACgv.H

Chain	Residue	Details
Q	PHE540-HIS549

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	12
Details	BINDING: BINDING => ECO:0000255

Chain	Residue	Details
Q	CYS72
S	CSX75
S	CYS543
S	CYS546
B	CYS20
B	CYS114
B	CYS147
B	HIS184
B	CYS187
B	CYS212
B	CYS218
Q	CSX75
B	CYS227
B	CYS245
B	CYS248
C	CYS17
C	CYS20
C	CYS114
C	CYS147
C	HIS184
C	CYS187
C	CYS212
Q	CYS543
C	CYS218
C	CYS227
C	CYS245
C	CYS248
Q	CYS546
R	CYS72
R	CSX75
R	CYS543
R	CYS546
S	CYS72

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)