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2BMO
Biol. Unit 1
Info
Asym.Unit (254 KB)
Biol.Unit 1 (730 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF NITROBENZENE DIOXYGENASE
Authors
:
R. Friemann, M. M. Ivkovic-Jensen, D. J. Lessner, C. Yu, D. T. Gibson, R. E. Parales, H. Eklund, S. Ramaswamy
Date
:
15 Mar 05 (Deposition) - 04 May 05 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (3x)
Keywords
:
Nitrobenzene Dioxygenase, Crystal Structure, Nitroarene, Rieske Non-Heme Dioxygenase, Substrate Specificity Iron- Sulfur, Metal-Binding, Nad, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Friemann, M. M. Ivkovic-Jensen, D. J. Lessner, C. Yu, D. T. Gibson, R. E. Parales, H. Eklund, S. Ramaswamy
Structural Insight Into The Dioxygenation Of Nitroarene Compounds: The Crystal Structure Of Nitrobenzene Dioxygenase
J. Mol. Biol. V. 348 1139 2005
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Hetero Components
(3, 63)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
2c: ETHANOL (EOHc)
2d: ETHANOL (EOHd)
2e: ETHANOL (EOHe)
2f: ETHANOL (EOHf)
2g: ETHANOL (EOHg)
2h: ETHANOL (EOHh)
2i: ETHANOL (EOHi)
2j: ETHANOL (EOHj)
2k: ETHANOL (EOHk)
2l: ETHANOL (EOHl)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3a: FE (III) ION (FEa)
5a: NICKEL (II) ION (NIa)
5b: NICKEL (II) ION (NIb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
24
Ligand/Ion
1,2-ETHANEDIOL
2
EOH
36
Ligand/Ion
ETHANOL
3
FE
-1
Ligand/Ion
FE (III) ION
4
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
NI
-1
Ligand/Ion
NICKEL (II) ION
[
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Sites
(24, 24)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:206 , HIS A:211 , ASP A:360 , EDO A:1442 , HOH A:2423
BINDING SITE FOR RESIDUE FE A1441
02
AC2
SOFTWARE
HIS B:14 , GLU B:18 , GLU B:160 , HOH B:2055 , HOH B:2056 , HOH B:2269
BINDING SITE FOR RESIDUE NI B1195
03
AC3
SOFTWARE
HIS B:56 , EDO B:1197 , HOH B:2003 , HOH B:2015 , HOH B:2140
BINDING SITE FOR RESIDUE NI B1196
04
AC4
SOFTWARE
CYS A:79 , HIS A:81 , ARG A:82 , CYS A:99 , TYR A:101 , HIS A:102 , TRP A:104
BINDING SITE FOR RESIDUE FES A1440
05
AC5
SOFTWARE
ASN A:199 , PHE A:200 , ASP A:203 , HIS A:206 , ASN A:295 , ASP A:360 , FE A:1441 , HOH A:2423
BINDING SITE FOR RESIDUE EDO A1442
06
AC6
SOFTWARE
LYS A:54 , GLU A:90 , PRO A:184 , LYS A:186 , TRP A:325 , EOH A:1445 , HOH A:2324 , GLU B:70 , ARG B:183
BINDING SITE FOR RESIDUE EDO A1443
07
AC7
SOFTWARE
LYS A:30 , ARG A:35 , ASP A:151
BINDING SITE FOR RESIDUE EDO A1444
08
AC8
SOFTWARE
TYR A:174 , MET B:2 , ASN B:4 , GLU B:7 , HIS B:56 , NI B:1196 , HOH B:2003 , HOH B:2015 , HOH B:2140 , HOH B:2299 , HOH B:2300
BINDING SITE FOR RESIDUE EDO B1197
09
AC9
SOFTWARE
TYR B:88 , GLN B:102 , LEU B:191 , VAL B:192 , PHE B:193 , HOH B:2301 , HOH B:2302
BINDING SITE FOR RESIDUE EDO B1198
10
BC1
SOFTWARE
THR B:35 , THR B:39 , VAL B:120 , ASN B:122 , VAL B:123 , HOH B:2303 , HOH B:2304
BINDING SITE FOR RESIDUE EDO B1199
11
BC2
SOFTWARE
ASP B:46 , ARG B:115 , PHE B:116 , HOH B:2305 , HOH B:2306
BINDING SITE FOR RESIDUE EDO B1200
12
BC3
SOFTWARE
PRO A:47 , SER A:48 , ASP A:51 , HOH A:2060 , ARG B:78 , TYR B:79 , GLN B:80 , HOH B:2307
BINDING SITE FOR RESIDUE EDO B1201
13
BC4
SOFTWARE
LYS A:54 , LYS A:56 , GLU A:61 , GLU A:90 , LYS A:186 , TRP A:325 , EDO A:1443 , GLU B:149 , HOH B:2250
BINDING SITE FOR RESIDUE EOH A1445
14
BC5
SOFTWARE
SER A:141 , PHE A:142 , HIS A:143 , HOH A:2190 , HOH A:2424 , GLU B:17
BINDING SITE FOR RESIDUE EOH A1446
15
BC6
SOFTWARE
ASP A:163 , TYR A:392 , GLY A:393 , PRO A:398 , GLY A:399 , HOH A:2395
BINDING SITE FOR RESIDUE EOH A1447
16
BC7
SOFTWARE
HIS A:88 , ALA A:89 , HOH A:2061 , ASN B:111 , HOH B:2218
BINDING SITE FOR RESIDUE EOH A1448
17
BC8
SOFTWARE
ARG A:288 , HOH A:2303 , HOH A:2426
BINDING SITE FOR RESIDUE EOH A1449
18
BC9
SOFTWARE
VAL A:188 , GLN B:186 , THR B:187 , HIS B:188
BINDING SITE FOR RESIDUE EOH B1202
19
CC1
SOFTWARE
LEU B:71 , PRO B:112 , LYS B:113 , ALA B:146 , ARG B:147 , ARG B:148
BINDING SITE FOR RESIDUE EOH B1203
20
CC2
SOFTWARE
GLU B:17 , GLU B:18 , ARG B:21 , HOH B:2308
BINDING SITE FOR RESIDUE EOH B1204
21
CC3
SOFTWARE
ASN A:93 , GLU B:76 , ARG B:77 , ARG B:78 , TYR B:79
BINDING SITE FOR RESIDUE EOH B1205
22
CC4
SOFTWARE
TRP A:166 , ARG A:286 , HOH A:2299 , ASN B:4 , GLN B:6
BINDING SITE FOR RESIDUE EOH B1206
23
CC5
SOFTWARE
PRO B:60 , LYS B:164 , LYS B:172
BINDING SITE FOR RESIDUE EOH B1207
24
CC6
SOFTWARE
HIS B:14
BINDING SITE FOR RESIDUE EOH B1208
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(, 0)
Info
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;
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End label:
Sorry, no Info available
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2bmoa1 (A:3-152)
2a: SCOP_d2bmob1 (B:1-194)
3a: SCOP_d2bmoa2 (A:153-439)
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(
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Folds
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(
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Superfamilies
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(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
ISP domain
(115)
Superfamily
:
ISP domain
(115)
Family
:
Ring hydroxylating alpha subunit ISP domain
(40)
Protein domain
:
Nitrobenzene dioxygenase alpha subunit, NBDO-alpha
(3)
Comamonas sp. JS765 [TaxId: 58226]
(3)
1a
d2bmoa1
A:3-152
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Cystatin-like
(403)
Superfamily
:
NTF2-like
(231)
Family
:
Ring hydroxylating beta subunit
(46)
Protein domain
:
Nitrobenzene dioxygenase beta subunit, NBDO-beta
(1)
Comamonas sp. JS765 [TaxId: 58226]
(1)
2a
d2bmob1
B:1-194
Fold
:
TBP-like
(289)
Superfamily
:
Bet v1-like
(158)
Family
:
Ring hydroxylating alpha subunit catalytic domain
(42)
Protein domain
:
Nitrobenzene dioxygenase alpha subunit, NBDO-alpha
(3)
Comamonas sp. JS765 [TaxId: 58226]
(3)
3a
d2bmoa2
A:153-439
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2bmoA01 (A:3-33,A:163-439)
2a: CATH_2bmoB00 (B:1-194)
3a: CATH_2bmoA02 (A:34-162)
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Homologous Superfamilies
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(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
(24)
Homologous Superfamily
:
Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1
(24)
Comamonas sp.. Organism_taxid: 58226. Strain: js765.
(3)
1a
2bmoA01
A:3-33,A:163-439
Architecture
:
Roll
(3276)
Topology
:
Nuclear Transport Factor 2; Chain: A,
(517)
Homologous Superfamily
:
[code=3.10.450.50, no name defined]
(113)
Comamonas sp.. Organism_taxid: 58226. Strain: js765.
(3)
2a
2bmoB00
B:1-194
Class
:
Mainly Beta
(13760)
Architecture
:
3-layer Sandwich
(102)
Topology
:
Rieske Iron-sulfur Protein
(99)
Homologous Superfamily
:
'Rieske'-like iron-sulphur domains
(99)
Comamonas sp.. Organism_taxid: 58226. Strain: js765.
(3)
3a
2bmoA02
A:34-162
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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