2HMK

Crystal Structure of Naphthalene 1,2-Dioxygenase Bound to Phenanthrene

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005506	molecular_function	iron ion binding
A	0016491	molecular_function	oxidoreductase activity
A	0018625	molecular_function	naphthalene 1,2-dioxygenase activity
A	0046872	molecular_function	metal ion binding
A	0051213	molecular_function	dioxygenase activity
A	0051536	molecular_function	iron-sulfur cluster binding
A	0051537	molecular_function	2 iron, 2 sulfur cluster binding
B	0016491	molecular_function	oxidoreductase activity
B	0019380	biological_process	3-phenylpropionate catabolic process
B	0051213	molecular_function	dioxygenase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE FE A 451

Chain	Residue
A	HIS208
A	HIS213
A	ASP362
A	HOH923

---

site_id	AC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE SO4 B 195

Chain	Residue
B	HOH880
B	GLN63
B	GLN65
B	HOH790
B	HOH820
B	HOH871

---

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 B 196

Chain	Residue
B	GLY59
B	SER60
B	GLU167
B	LYS172

---

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE SO4 A 452

Chain	Residue
A	TRP439
A	HIS440
A	EDO716
A	HOH855
A	HOH875

---

site_id	AC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE SO4 A 453

Chain	Residue
A	LEU128
A	LYS130
A	LYS131
A	HOH1005

---

site_id	AC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE SO4 B 197

Chain	Residue
A	THR87
A	THR368
A	HOH805
A	HOH812
A	HOH952
B	ARG148
B	HOH834

---

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE FES A 454

Chain	Residue
A	CYS81
A	HIS83
A	ARG84
A	CYS101
A	TYR103
A	HIS104
A	GLY105
A	TRP106

---

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PEY A 701

Chain	Residue
A	ASN201
A	ASP205
A	PHE224
A	ASN297
A	HOH923

---

site_id	AC9
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO B 702

Chain	Residue
B	ASP46
B	ARG115
B	PHE116
B	EDO721
B	HOH781
B	HOH856

---

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 703

Chain	Residue
B	GLU83
B	ALA84
B	ASN86
B	HOH816
B	HOH864

---

site_id	BC2
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 706

Chain	Residue
B	TYR88
B	GLN102
B	MET191
B	VAL192
B	PHE193
B	HOH730
B	HOH738

---

site_id	BC3
Number of Residues	10
Details	BINDING SITE FOR RESIDUE EDO A 709

Chain	Residue
A	LEU31
A	PHE35
A	ALA36
A	MET59
A	GLY60
A	ILE61
A	ASP62
A	PHE152
A	TYR376
A	GLN377

---

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 710

Chain	Residue
A	HIS18
A	VAL80
A	CYS81
A	ARG82
A	SER381
A	ASP382
A	LEU383
A	HOH747
A	HOH779

---

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 711

Chain	Residue
A	GLU24
A	LYS374
A	EDO712
A	HOH770
A	HOH909

---

site_id	BC6
Number of Residues	9
Details	BINDING SITE FOR RESIDUE EDO A 712

Chain	Residue
A	GLY22
A	GLN28
A	LYS374
A	ARG379
A	EDO711
A	HOH764
A	HOH770
A	HOH858
A	HOH909

---

site_id	BC7
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 714

Chain	Residue
A	PRO118
A	PHE119
A	HOH954
A	HOH1098

---

site_id	BC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 715

Chain	Residue
A	ASP346
A	HOH749
A	HOH896
B	ASN82
B	HOH864
A	ARG342

---

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 716

Chain	Residue
A	GLY164
A	ASP165
A	SO4452

---

site_id	CC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 717

Chain	Residue
A	TRP168
A	VAL398
A	PRO400
A	THR438
A	HIS440
A	HOH768
A	HOH855
A	HOH930

---

site_id	CC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 718

Chain	Residue
A	HOH1100
B	ASN91
B	GLN94
B	HOH833

---

site_id	CC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 719

Chain	Residue
A	TRP254
A	ARG290
A	TYR399
A	HOH939

---

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 720

Chain	Residue
A	THR56
A	GLU92
A	PRO186
A	LYS188
A	HOH1027
B	GLU70
B	ARG183

---

site_id	CC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO B 721

Chain	Residue
B	ALA158
B	GLU160
B	PHE177
B	VAL178
B	ASP179
B	EDO702
B	HOH755

---

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 722

Chain	Residue
A	VAL190
B	GLN186
B	THR187
B	HIS188

---

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 723

Chain	Residue
A	PHE272
A	LYS276
A	ARG279
A	HOH1002
A	HOH1092

---

site_id	CC8
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 724

Chain	Residue
A	HIS176
A	SER177
A	LYS276
A	ARG279
A	LEU280
A	ASP335

---

site_id	CC9
Number of Residues	8
Details	BINDING SITE FOR RESIDUE EDO A 725

Chain	Residue
A	ASN4
A	HIS29
A	THR33
A	VAL424
A	SER425
A	SER426
A	SER427
A	HOH1180

---

site_id	DC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 726

Chain	Residue
A	LYS136
A	GLN377
A	HOH752

---

Functional Information from PROSITE/UniProt

site_id	PS00570
Number of Residues	24
Details	RING_HYDROXYL_ALPHA Bacterial ring hydroxylating dioxygenases alpha-subunit signature. CrHRGktlvsveaGNakgfvCsYH

Chain	Residue	Details
A	CYS81-HIS104

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	98
Details	Domain: {"description":"Rieske","evidences":[{"source":"PROSITE-ProRule","id":"PRU00628","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"16980501","evidenceCode":"ECO:0000269"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"OCT-2012","submissionDatabase":"PDB data bank","title":"Naphthalene 1,2-Dioxygenase bound to thioanisole.","authors":["Ferraro D.J.","Ramaswamy S."]}},{"source":"PDB","id":"2HMJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HMK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HML","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HMM","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HMN","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HMO","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HJL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HKV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM0","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM1","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM2","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM4","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM5","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM6","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM7","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4HM8","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1ndo

Chain	Residue	Details
A	HIS208
A	ASP205

---

site_id	CSA2
Number of Residues	1
Details	Annotated By Reference To The Literature 1ndo

Chain	Residue	Details
A	HIS104

---