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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6Z8O

Structure of [NiFeSe] hydrogenase G491A variant from Desulfovibrio vulgaris Hildenborough pressurized with Krypton gas - structure G491A-Kr

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0009375	cellular_component	ferredoxin hydrogenase complex
A	0051536	molecular_function	iron-sulfur cluster binding
B	0005515	molecular_function	protein binding
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0016151	molecular_function	nickel cation binding
B	0016491	molecular_function	oxidoreductase activity
B	0046872	molecular_function	metal ion binding
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0009375	cellular_component	ferredoxin hydrogenase complex
C	0051536	molecular_function	iron-sulfur cluster binding
D	0005515	molecular_function	protein binding
D	0008901	molecular_function	ferredoxin hydrogenase activity
D	0016151	molecular_function	nickel cation binding
D	0016491	molecular_function	oxidoreductase activity
D	0046872	molecular_function	metal ion binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue SF4 A 301

Chain	Residue
A	HIS208
A	CYS211
A	CYS232
A	ARG233
A	TYR234
A	CYS238
A	GLY240

site_id	AC2
Number of Residues	8
Details	binding site for residue SF4 A 302

Chain	Residue
A	CYS259
A	CYS265
A	ILE266
A	CYS268
A	VAL269
B	ARG182
A	CYS247
A	TRP252

site_id	AC3
Number of Residues	11
Details	binding site for residue SF4 A 303

Chain	Residue
A	CYS18
A	CYS21
A	GLU77
A	GLY119
A	THR120
A	CYS121
A	GLY158
A	CYS159
A	6ML304
B	ARG73
B	HIS185

site_id	AC4
Number of Residues	13
Details	binding site for residue 6ML A 304

Chain	Residue
A	CYS18
A	THR19
A	GLY20
A	CYS21
A	GLU77
A	GLY78
A	THR120
A	CYS121
A	GLY158
A	CYS159
A	SF4303
B	ARG73
B	HIS185

site_id	AC5
Number of Residues	1
Details	binding site for residue KR A 305

Chain	Residue
B	PHE139

site_id	AC6
Number of Residues	1
Details	binding site for residue KR A 306

Chain	Residue
A	PHE73

site_id	AC7
Number of Residues	1
Details	binding site for residue KR A 307

Chain	Residue
A	VAL170

site_id	AC8
Number of Residues	1
Details	binding site for residue KR A 309

Chain	Residue
A	ALA114

site_id	AC9
Number of Residues	1
Details	binding site for residue KR A 310

Chain	Residue
A	LEU26

site_id	AD1
Number of Residues	10
Details	binding site for residue FCO B 501

Chain	Residue
B	CYS78
B	ALA420
B	PRO421
B	ARG422
B	ALA444
B	SER445
B	SEC489
B	CYS492
B	NI502
B	H2S504

site_id	AD2
Number of Residues	6
Details	binding site for residue NI B 502

Chain	Residue
B	CYS75
B	CYS78
B	SEC489
B	CYS492
B	FCO501
B	H2S504

site_id	AD3
Number of Residues	6
Details	binding site for residue FE2 B 503

Chain	Residue
B	GLU56
B	GLU282
B	ILE441
B	HIS495
B	HOH603
B	HOH608

site_id	AD4
Number of Residues	6
Details	binding site for residue CL B 505

Chain	Residue
B	CYS78
B	THR80
B	ALA81
B	PHE110
B	ASN113
B	PRO421

site_id	AD5
Number of Residues	2
Details	binding site for residue KR B 506

Chain	Residue
B	PHE122
B	GLY158

site_id	AD6
Number of Residues	2
Details	binding site for residue KR B 507

Chain	Residue
B	TYR162
B	KR508

site_id	AD7
Number of Residues	2
Details	binding site for residue KR B 508

Chain	Residue
B	HIS124
B	KR507

site_id	AD8
Number of Residues	1
Details	binding site for residue KR B 509

Chain	Residue
B	VAL131

site_id	AD9
Number of Residues	5
Details	binding site for residue SF4 C 301

Chain	Residue
C	HIS208
C	CYS211
C	CYS232
C	CYS238
C	VAL260

site_id	AE1
Number of Residues	8
Details	binding site for residue SF4 C 302

Chain	Residue
C	CYS247
C	TRP252
C	CYS259
C	CYS265
C	ILE266
C	CYS268
C	VAL269
D	ARG182

site_id	AE2
Number of Residues	10
Details	binding site for residue SF4 C 303

Chain	Residue
C	6ML304
D	ARG73
D	HIS185
C	CYS18
C	CYS21
C	GLY119
C	THR120
C	CYS121
C	GLY158
C	CYS159

site_id	AE3
Number of Residues	14
Details	binding site for residue 6ML C 304

Chain	Residue
C	GLY17
C	CYS18
C	THR19
C	GLY20
C	CYS21
C	GLU77
C	GLY78
C	GLY119
C	THR120
C	CYS121
C	GLY158
C	CYS159
C	SF4303
D	HIS185

site_id	AE4
Number of Residues	1
Details	binding site for residue KR C 306

Chain	Residue
C	PHE73

site_id	AE5
Number of Residues	1
Details	binding site for residue KR C 307

Chain	Residue
C	ALA114

site_id	AE6
Number of Residues	1
Details	binding site for residue KR C 308

Chain	Residue
C	VAL170

site_id	AE7
Number of Residues	3
Details	binding site for residue KR C 310

Chain	Residue
C	PRO152
C	VAL154
C	VAL189

site_id	AE8
Number of Residues	11
Details	binding site for residue FCO D 501

Chain	Residue
D	CYS78
D	ALA420
D	PRO421
D	ARG422
D	LEU425
D	ALA444
D	SER445
D	SEC489
D	CYS492
D	NI502
D	H2S504

site_id	AE9
Number of Residues	6
Details	binding site for residue NI D 502

Chain	Residue
D	CYS75
D	CYS78
D	SEC489
D	CYS492
D	FCO501
D	H2S504

site_id	AF1
Number of Residues	6
Details	binding site for residue FE2 D 503

Chain	Residue
D	GLU56
D	GLU282
D	LYS317
D	ILE441
D	HIS495
D	HOH604

site_id	AF2
Number of Residues	6
Details	binding site for residue CL D 505

Chain	Residue
D	CYS78
D	THR80
D	ALA81
D	PHE110
D	ASN113
D	PRO421

site_id	AF3
Number of Residues	2
Details	binding site for residue KR D 506

Chain	Residue
D	TYR123
D	GLY158

site_id	AF4
Number of Residues	2
Details	binding site for residue KR D 507

Chain	Residue
D	VAL131
D	TYR162

site_id	AF5
Number of Residues	1
Details	binding site for residue KR D 508

Chain	Residue
D	TYR162

site_id	AF6
Number of Residues	13
Details	binding site for residues H2S B 504 and SEC B 489

Chain	Residue
B	GLU28
B	CYS75
B	CYS78
B	ARG422
B	SER445
B	ASP487
B	PRO488
B	LEU490
B	ALA491
B	CYS492
B	ALA493
B	FCO501
B	NI502

site_id	AF7
Number of Residues	13
Details	binding site for residues H2S B 504 and SEC B 489

Chain	Residue
B	GLU28
B	CYS75
B	CYS78
B	ARG422
B	SER445
B	ASP487
B	PRO488
B	LEU490
B	ALA491
B	CYS492
B	ALA493
B	FCO501
B	NI502

site_id	AF8
Number of Residues	13
Details	binding site for residues H2S D 504 and SEC D 489

Chain	Residue
D	GLU28
D	CYS75
D	CYS78
D	ARG422
D	SER445
D	ASP487
D	PRO488
D	LEU490
D	ALA491
D	CYS492
D	ALA493
D	FCO501
D	NI502

site_id	AF9
Number of Residues	13
Details	binding site for residues H2S D 504 and SEC D 489

Chain	Residue
D	GLU28
D	CYS75
D	CYS78
D	ARG422
D	SER445
D	ASP487
D	PRO488
D	LEU490
D	ALA491
D	CYS492
D	ALA493
D	FCO501
D	NI502

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
B	ARG53-CYS78

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

Chain	Residue	Details
B	PHE486-HIS495

224004

PDB entries from 2024-08-21

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