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Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3AYX

Membrane-bound respiratory [NiFe] hydrogenase from Hydrogenovibrio marinus in an H2-reduced condition

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005886	cellular_component	plasma membrane
A	0008901	molecular_function	ferredoxin hydrogenase activity
A	0016151	molecular_function	nickel cation binding
A	0016491	molecular_function	oxidoreductase activity
A	0046872	molecular_function	metal ion binding
B	0008901	molecular_function	ferredoxin hydrogenase activity
B	0009375	cellular_component	ferredoxin hydrogenase complex
B	0051536	molecular_function	iron-sulfur cluster binding
C	0005886	cellular_component	plasma membrane
C	0008901	molecular_function	ferredoxin hydrogenase activity
C	0016151	molecular_function	nickel cation binding
C	0016491	molecular_function	oxidoreductase activity
C	0046872	molecular_function	metal ion binding
D	0008901	molecular_function	ferredoxin hydrogenase activity
D	0009375	cellular_component	ferredoxin hydrogenase complex
D	0051536	molecular_function	iron-sulfur cluster binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FE2 A 601

Chain	Residue
A	CYS79
A	CYS593
A	NI602
A	CMO603
A	CYN604
A	CYN605
A	O606
A	O609
A	O610

site_id	AC2
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NI A 602

Chain	Residue
A	CYS76
A	CYS79
A	CYS590
A	CYS593
A	FE2601
A	O606
A	O607
A	O608
A	O609
A	O610

site_id	AC3
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CMO A 603

Chain	Residue
A	CYS79
A	CYS82
A	HIS83
A	ALA521
A	LEU526
A	VAL544
A	PRO545
A	CYS593
A	FE2601
A	CYN604
A	CYN605

site_id	AC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CYN A 604

Chain	Residue
A	CYS79
A	ALA521
A	PRO522
A	ARG523
A	FE2601
A	CMO603
A	CYN605
A	O606

site_id	AC5
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CYN A 605

Chain	Residue
A	ARG523
A	VAL544
A	PRO545
A	THR546
A	CYS590
A	CYS593
A	FE2601
A	CMO603
A	CYN604
A	O606

site_id	AC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE O A 606

Chain	Residue
A	CYS79
A	ARG523
A	CYS590
A	CYS593
A	FE2601
A	NI602
A	CYN604
A	CYN605
A	O607
A	O608
A	O609
A	O610

site_id	AC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE O A 607

Chain	Residue
A	GLU28
A	CYS76
A	CYS590
A	ALA592
A	CYS593
A	NI602
A	O606
A	O608
A	O609
A	O610

site_id	AC8
Number of Residues	10
Details	BINDING SITE FOR RESIDUE O A 608

Chain	Residue
A	GLU28
A	CYS76
A	CYS590
A	LEU591
A	ALA592
A	CYS593
A	NI602
A	O606
A	O607
A	O610

site_id	AC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE O A 609

Chain	Residue
A	CYS76
A	CYS79
A	CYS590
A	CYS593
A	FE2601
A	NI602
A	O606
A	O607
A	O610

site_id	BC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE O A 610

Chain	Residue
A	CYS76
A	CYS79
A	CYS590
A	CYS593
A	FE2601
A	NI602
A	O606
A	O607
A	O608
A	O609

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE GOL A 702

Chain	Residue
A	LYS310
A	GLN319
A	ASP482
A	HOH922
A	HOH1551

site_id	BC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GOL A 703

Chain	Residue
A	ILE242
A	ASN243
A	ILE244
A	ASP245
A	GLY246
A	SER496
A	HOH1420
B	ARG220

site_id	BC4
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG A 701

Chain	Residue
A	GLU57
A	CYS542
A	HIS596
A	HOH614
A	HOH626
A	HOH907

site_id	BC5
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F4S B 301

Chain	Residue
B	GLU22
B	CYS23
B	THR24
B	CYS25
B	CYS26
B	SER120
B	CYS121
B	CYS126
B	CYS158

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F3S B 308

Chain	Residue
A	LYS227
B	THR235
B	ASN237
B	CYS239
B	TRP244
B	CYS258
B	ILE259
B	CYS261

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SF4 B 309

Chain	Residue
B	HIS196
B	CYS199
B	ARG202
B	CYS224
B	LEU225
B	CYS230

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE MG C 701

Chain	Residue
C	GLU57
C	CYS542
C	HIS596
C	HOH600
C	HOH750
C	HOH825

site_id	BC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE FE2 C 601

Chain	Residue
C	CYS79
C	CYS593
C	NI602
C	CMO603
C	CYN604
C	CYN605
C	O606
C	O609
C	O610

site_id	CC1
Number of Residues	10
Details	BINDING SITE FOR RESIDUE NI C 602

Chain	Residue
C	CYS76
C	CYS79
C	CYS590
C	CYS593
C	FE2601
C	O606
C	O607
C	O608
C	O609
C	O610

site_id	CC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE CMO C 603

Chain	Residue
C	CYS79
C	CYS82
C	HIS83
C	ALA521
C	LEU526
C	VAL544
C	PRO545
C	CYS593
C	FE2601
C	CYN604
C	CYN605

site_id	CC3
Number of Residues	8
Details	BINDING SITE FOR RESIDUE CYN C 604

Chain	Residue
C	CYS79
C	ALA521
C	PRO522
C	ARG523
C	FE2601
C	CMO603
C	CYN605
C	O606

site_id	CC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE CYN C 605

Chain	Residue
C	ARG523
C	VAL544
C	PRO545
C	THR546
C	CYS590
C	CYS593
C	FE2601
C	CMO603
C	CYN604
C	O606

site_id	CC5
Number of Residues	12
Details	BINDING SITE FOR RESIDUE O C 606

Chain	Residue
C	CYS79
C	ARG523
C	CYS590
C	CYS593
C	FE2601
C	NI602
C	CYN604
C	CYN605
C	O607
C	O608
C	O609
C	O610

site_id	CC6
Number of Residues	10
Details	BINDING SITE FOR RESIDUE O C 607

Chain	Residue
C	GLU28
C	CYS76
C	CYS590
C	ALA592
C	CYS593
C	NI602
C	O606
C	O608
C	O609
C	O610

site_id	CC7
Number of Residues	10
Details	BINDING SITE FOR RESIDUE O C 608

Chain	Residue
C	GLU28
C	CYS76
C	CYS590
C	LEU591
C	ALA592
C	CYS593
C	NI602
C	O606
C	O607
C	O610

site_id	CC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE O C 609

Chain	Residue
C	CYS76
C	CYS79
C	CYS590
C	CYS593
C	FE2601
C	NI602
C	O606
C	O607
C	O610

site_id	CC9
Number of Residues	10
Details	BINDING SITE FOR RESIDUE O C 610

Chain	Residue
C	CYS76
C	CYS79
C	CYS590
C	CYS593
C	FE2601
C	NI602
C	O606
C	O607
C	O608
C	O609

site_id	DC1
Number of Residues	6
Details	BINDING SITE FOR RESIDUE GOL C 702

Chain	Residue
C	LYS310
C	GLN319
C	TYR475
C	ASP482
C	HOH847
C	HOH1422

site_id	DC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GOL C 703

Chain	Residue
C	ILE242
C	ASN243
C	ILE244
C	ASP245
C	GLY246
C	SER496
D	ARG220

site_id	DC3
Number of Residues	9
Details	BINDING SITE FOR RESIDUE F4S D 301

Chain	Residue
D	GLU22
D	CYS23
D	THR24
D	CYS25
D	CYS26
D	SER120
D	CYS121
D	CYS126
D	CYS158

site_id	DC4
Number of Residues	8
Details	BINDING SITE FOR RESIDUE F3S D 308

Chain	Residue
C	LYS227
D	THR235
D	ASN237
D	CYS239
D	TRP244
D	CYS258
D	ILE259
D	CYS261

site_id	DC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SF4 D 309

Chain	Residue
D	HIS196
D	CYS199
D	ARG202
D	CYS224
D	LEU225
D	CYS230

Functional Information from PROSITE/UniProt

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

Chain	Residue	Details
A	ARG54-CYS79

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

Chain	Residue	Details
A	PHE587-HIS596

245663

PDB entries from 2025-12-03

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