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2BMQ
Biol. Unit 1
Info
Asym.Unit (129 KB)
Biol.Unit 1 (358 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF NITROBENZENE DIOXYGENASE IN COMPLEX WITH NITROBENZENE
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
:
1.55
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
(4, 42)
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)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
2c: ETHANOL (EOHc)
2d: ETHANOL (EOHd)
2e: ETHANOL (EOHe)
2f: ETHANOL (EOHf)
4a: FE2/S2 (INORGANIC) CLUSTER (FESa)
3a: FE (III) ION (FEa)
5a: NITROBENZENE (NBZa)
6a: NICKEL (II) ION (NIa)
6b: NICKEL (II) ION (NIb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
18
Ligand/Ion
1,2-ETHANEDIOL
2
EOH
18
Ligand/Ion
ETHANOL
3
FE
-1
Ligand/Ion
FE (III) ION
4
FES
3
Ligand/Ion
FE2/S2 (INORGANIC) CLUSTER
5
NBZ
3
Ligand/Ion
NITROBENZENE
6
NI
-1
Ligand/Ion
NICKEL (II) ION
[
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Sites
(17, 17)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:206 , HIS A:211 , ASP A:360 , HOH A:2227 , HOH A:2401
BINDING SITE FOR RESIDUE FE A1441
02
AC2
SOFTWARE
HIS B:14 , GLU B:18 , GLU B:160 , HOH B:2060 , HOH B:2061 , HOH B:2256
BINDING SITE FOR RESIDUE NI B1195
03
AC3
SOFTWARE
HIS B:56 , EDO B:1197 , HOH B:2001 , HOH B:2017 , HOH B:2291
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 , VAL A:207 , ASN A:258 , PHE A:293 , LEU A:305 , HOH A:2401
BINDING SITE FOR RESIDUE NBZ A1442
06
AC6
SOFTWARE
LYS A:30 , ARG A:35 , ASP A:151 , SER A:425
BINDING SITE FOR RESIDUE EDO A1443
07
AC7
SOFTWARE
LYS A:54 , GLU A:90 , PRO A:184 , LYS A:186 , EOH A:1445 , EOH A:1446 , GLU B:70 , ARG B:183
BINDING SITE FOR RESIDUE EDO A1444
08
AC8
SOFTWARE
TYR A:174 , MET B:2 , ASN B:4 , HIS B:56 , NI B:1196 , HOH B:2001 , HOH B:2291 , HOH B:2292 , HOH B:2293
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:2294 , HOH B:2295
BINDING SITE FOR RESIDUE EDO B1198
10
BC1
SOFTWARE
PRO A:47 , SER A:48 , ASP A:51 , HOH A:2051 , ARG B:78 , TYR B:79 , GLN B:80 , LEU B:81 , HOH B:2296
BINDING SITE FOR RESIDUE EDO B1199
11
BC2
SOFTWARE
THR B:35 , THR B:39 , VAL B:120 , ASN B:122 , VAL B:123 , HOH B:2217
BINDING SITE FOR RESIDUE EDO B1200
12
BC3
SOFTWARE
LEU A:45 , VAL A:53 , PRO A:183 , PRO A:184 , TYR A:327 , EDO A:1444 , HOH A:2308 , GLU B:70 , HOH B:2163
BINDING SITE FOR RESIDUE EOH A1445
13
BC4
SOFTWARE
LYS A:54 , LYS A:56 , GLU A:61 , LYS A:186 , TRP A:325 , EDO A:1444 , GLU B:149 , HOH B:2238
BINDING SITE FOR RESIDUE EOH A1446
14
BC5
SOFTWARE
ASN A:5 , LEU A:6 , SER A:8 , THR A:13 , GLN A:14 , LYS A:15 , ASP A:380
BINDING SITE FOR RESIDUE EOH A1447
15
BC6
SOFTWARE
HIS A:88 , ALA A:89 , HOH A:2053 , ASN B:111 , HOH B:2203
BINDING SITE FOR RESIDUE EOH A1448
16
BC7
SOFTWARE
LEU B:71 , PRO B:112 , LYS B:113 , ALA B:146 , ARG B:147 , ARG B:148
BINDING SITE FOR RESIDUE EOH B1201
17
BC8
SOFTWARE
ASP B:46 , ARG B:115 , PHE B:116 , HOH B:2234
BINDING SITE FOR RESIDUE EOH B1202
[
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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
All PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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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_d2bmqa1 (A:3-152)
2a: SCOP_d2bmqb_ (B:)
3a: SCOP_d2bmqa2 (A:153-439)
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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
d2bmqa1
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
:
automated matches
(12)
Comamonas sp. [TaxId: 58226]
(2)
2a
d2bmqb_
B:
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
d2bmqa2
A:153-439
[
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CATH Domains
(3, 3)
Info
all CATH domains
1a: CATH_2bmqA01 (A:3-33,A:163-439)
2a: CATH_2bmqB00 (B:1-194)
3a: CATH_2bmqA02 (A:34-162)
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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
2bmqA01
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
2bmqB00
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
2bmqA02
A:34-162
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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