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2BOY
Asym. Unit
Info
Asym.Unit (375 KB)
Biol.Unit 1 (98 KB)
Biol.Unit 2 (97 KB)
Biol.Unit 3 (95 KB)
Biol.Unit 4 (96 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF 3-CHLOROCATECHOL 1,2-DIOXYGENASE FROM RHODOCOCCUS OPACUS 1CP
Authors
:
M. Ferraroni, I. P. Solyanikova, M. P. Kolomytseva, A. Scozzafava, L. A. Golovleva, F. Briganti
Date
:
15 Apr 05 (Deposition) - 24 Aug 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Biol. Unit 3: C,G (1x)
Biol. Unit 4: D,H (1x)
Keywords
:
Beta Barrel, Oxidoreductase, Dioxygenase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Ferraroni, M. P. Kolomytseva, I. P. Solyanikova, A. Scozzafava, L. A. Golovleva, F. Briganti
Crystal Structure Of 3-Chlorocatechol 1, 2-Dioxygenase Key Enzyme Of A New Modified Ortho-Pathway From The Gram-Positive Rhodococcus Opacus 1Cp Grown On 2-Chlorophenol
J. Mol. Biol. V. 360 788 2006
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 40)
Info
All Hetero Components
1a: BENZHYDROXAMIC ACID (BHOa)
1b: BENZHYDROXAMIC ACID (BHOb)
1c: BENZHYDROXAMIC ACID (BHOc)
1d: BENZHYDROXAMIC ACID (BHOd)
1e: BENZHYDROXAMIC ACID (BHOe)
1f: BENZHYDROXAMIC ACID (BHOf)
1g: BENZHYDROXAMIC ACID (BHOg)
1h: BENZHYDROXAMIC ACID (BHOh)
2a: FE (III) ION (FEa)
2b: FE (III) ION (FEb)
2c: FE (III) ION (FEc)
2d: FE (III) ION (FEd)
2e: FE (III) ION (FEe)
2f: FE (III) ION (FEf)
2g: FE (III) ION (FEg)
2h: FE (III) ION (FEh)
3a: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPa)
3b: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPb)
3c: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPc)
3d: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPd)
3e: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPe)
3f: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPf)
3g: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPg)
3h: 2-(HEXADECANOYLOXY)-1-[(PHOSPHONOO... (LPPh)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
4c: MAGNESIUM ION (MGc)
4d: MAGNESIUM ION (MGd)
4e: MAGNESIUM ION (MGe)
4f: MAGNESIUM ION (MGf)
4g: MAGNESIUM ION (MGg)
4h: MAGNESIUM ION (MGh)
4i: MAGNESIUM ION (MGi)
4j: MAGNESIUM ION (MGj)
4k: MAGNESIUM ION (MGk)
4l: MAGNESIUM ION (MGl)
4m: MAGNESIUM ION (MGm)
4n: MAGNESIUM ION (MGn)
4o: MAGNESIUM ION (MGo)
4p: MAGNESIUM ION (MGp)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BHO
8
Ligand/Ion
BENZHYDROXAMIC ACID
2
FE
8
Ligand/Ion
FE (III) ION
3
LPP
8
Ligand/Ion
2-(HEXADECANOYLOXY)-1-[(PHOSPHONOOXY)METHYL]ETHYL HEXADECANOATE
4
MG
16
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(40, 40)
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)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
TYR A:133 , TYR A:167 , HIS A:191 , HIS A:193 , BHO A:1256
BINDING SITE FOR RESIDUE FE A1255
02
AC2
SOFTWARE
HOH A:2030 , HOH A:2088 , HOH A:2094 , HOH A:2095
BINDING SITE FOR RESIDUE MG A1258
03
AC3
SOFTWARE
HOH A:2028 , HOH A:2029 , HOH A:2033 , HOH A:2087 , HOH A:2090 , HOH A:2093
BINDING SITE FOR RESIDUE MG A1259
04
AC4
SOFTWARE
TYR B:133 , TYR B:167 , HIS B:191 , HIS B:193 , BHO B:1256
BINDING SITE FOR RESIDUE FE B1255
05
AC5
SOFTWARE
HOH B:2084 , HOH B:2085 , HOH B:2088 , HOH B:2090
BINDING SITE FOR RESIDUE MG B1258
06
AC6
SOFTWARE
HOH B:2026 , HOH B:2027 , HOH B:2030 , HOH B:2083 , HOH B:2089 , HOH B:2198
BINDING SITE FOR RESIDUE MG B1259
07
AC7
SOFTWARE
HOH B:2144 , HOH B:2145 , HOH G:2087
BINDING SITE FOR RESIDUE MG B1260
08
AC8
SOFTWARE
TYR C:133 , TYR C:167 , HIS C:191 , HIS C:193 , BHO C:1256
BINDING SITE FOR RESIDUE FE C1255
09
AC9
SOFTWARE
HOH C:2023 , HOH C:2024 , HOH C:2059 , HOH C:2166 , HOH C:2168
BINDING SITE FOR RESIDUE MG C1258
10
BC1
SOFTWARE
HOH C:2044 , HOH C:2073 , HOH C:2074 , HOH F:2151 , HOH F:2153 , HOH F:2155
BINDING SITE FOR RESIDUE MG C1259
11
BC2
SOFTWARE
HOH A:2171 , HOH C:2057 , HOH C:2060
BINDING SITE FOR RESIDUE MG C1260
12
BC3
SOFTWARE
HOH A:2157 , HOH A:2159 , HOH H:2100 , HOH H:2101
BINDING SITE FOR RESIDUE MG C1261
13
BC4
SOFTWARE
TYR D:133 , TYR D:167 , HIS D:191 , HIS D:193 , BHO D:1256
BINDING SITE FOR RESIDUE FE D1255
14
BC5
SOFTWARE
HOH D:2023 , HOH D:2024 , HOH D:2027 , HOH D:2076 , HOH D:2083
BINDING SITE FOR RESIDUE MG D1258
15
BC6
SOFTWARE
HOH D:2058 , HOH D:2143 , HOH D:2144 , HOH D:2150 , HOH E:2110 , HOH E:2111
BINDING SITE FOR RESIDUE MG D1259
16
BC7
SOFTWARE
TYR E:133 , TYR E:167 , HIS E:191 , HIS E:193 , BHO E:1256
BINDING SITE FOR RESIDUE FE E1255
17
BC8
SOFTWARE
HOH E:2036 , HOH E:2090
BINDING SITE FOR RESIDUE MG E1258
18
BC9
SOFTWARE
TYR F:133 , TYR F:167 , HIS F:191 , HIS F:193 , BHO F:1256 , HOH F:2169
BINDING SITE FOR RESIDUE FE F1255
19
CC1
SOFTWARE
HOH F:2032 , HOH F:2033 , HOH F:2036 , HOH F:2084 , HOH F:2088
BINDING SITE FOR RESIDUE MG F1258
20
CC2
SOFTWARE
TYR G:133 , TYR G:167 , HIS G:191 , HIS G:193 , BHO G:1256
BINDING SITE FOR RESIDUE FE G1255
21
CC3
SOFTWARE
HOH G:2022 , HOH G:2023 , HOH G:2025 , HOH G:2069 , HOH G:2071
BINDING SITE FOR RESIDUE MG G1258
22
CC4
SOFTWARE
TYR H:133 , TYR H:167 , HIS H:191 , HIS H:193 , BHO H:1256
BINDING SITE FOR RESIDUE FE H1255
23
CC5
SOFTWARE
HOH H:2030 , HOH H:2031 , HOH H:2081 , HOH H:2087 , HOH H:2174
BINDING SITE FOR RESIDUE MG H1258
24
CC6
SOFTWARE
SER D:66 , HOH D:2022 , HOH D:2026 , HOH D:2075 , HOH D:2079 , HOH D:2080 , HOH D:2081
BINDING SITE FOR RESIDUE MG H1259
25
CC7
SOFTWARE
LEU A:49 , VAL A:53 , PRO A:77 , TYR A:78 , TYR A:133 , TYR A:167 , ILE A:169 , ARG A:188 , HIS A:191 , HIS A:193 , GLN A:207 , FE A:1255 , HOH A:2266
BINDING SITE FOR RESIDUE BHO A1256
26
CC8
SOFTWARE
GLU A:30 , ALA A:33 , SER A:34 , TRP A:37 , LPP E:1257
BINDING SITE FOR RESIDUE LPP A1257
27
CC9
SOFTWARE
LEU B:49 , VAL B:53 , ILE B:74 , GLY B:76 , PRO B:77 , TYR B:78 , TYR B:133 , TYR B:167 , ILE B:169 , ARG B:188 , HIS B:191 , HIS B:193 , GLN B:207 , FE B:1255 , HOH B:2240
BINDING SITE FOR RESIDUE BHO B1256
28
DC1
SOFTWARE
ALA B:33 , SER B:34 , TRP B:37 , LEU B:178 , HOH B:2241 , THR F:6 , LEU F:51
BINDING SITE FOR RESIDUE LPP B1257
29
DC2
SOFTWARE
LEU C:49 , VAL C:53 , ILE C:74 , GLY C:76 , PRO C:77 , TYR C:78 , TYR C:133 , TYR C:167 , ARG C:188 , HIS C:191 , HIS C:193 , FE C:1255 , HOH C:2203
BINDING SITE FOR RESIDUE BHO C1256
30
DC3
SOFTWARE
GLU C:30 , SER C:34 , TRP C:37 , THR G:6 , LPP G:1257
BINDING SITE FOR RESIDUE LPP C1257
31
DC4
SOFTWARE
LEU D:49 , VAL D:53 , GLY D:76 , PRO D:77 , TYR D:78 , TYR D:133 , TYR D:167 , ARG D:188 , HIS D:191 , HIS D:193 , GLN D:207 , FE D:1255 , HOH D:2241
BINDING SITE FOR RESIDUE BHO D1256
32
DC5
SOFTWARE
GLU D:30 , ALA D:33 , SER D:34 , TRP D:37 , THR H:6 , LPP H:1257
BINDING SITE FOR RESIDUE LPP D1257
33
DC6
SOFTWARE
LEU E:49 , VAL E:53 , ILE E:74 , GLY E:76 , PRO E:77 , TYR E:78 , TYR E:133 , TYR E:167 , ARG E:188 , HIS E:191 , HIS E:193 , GLN E:207 , FE E:1255 , HOH E:2232
BINDING SITE FOR RESIDUE BHO E1256
34
DC7
SOFTWARE
ILE A:17 , LPP A:1257 , SER E:34 , HOH E:2233
BINDING SITE FOR RESIDUE LPP E1257
35
DC8
SOFTWARE
LEU F:49 , VAL F:53 , PRO F:77 , TYR F:78 , TYR F:133 , TYR F:167 , ILE F:169 , ARG F:188 , HIS F:191 , HIS F:193 , FE F:1255 , HOH F:2169 , HOH F:2229
BINDING SITE FOR RESIDUE BHO F1256
36
DC9
SOFTWARE
THR B:6 , ILE B:17 , SER F:34 , TRP F:37 , LEU F:178 , HOH F:2230
BINDING SITE FOR RESIDUE LPP F1257
37
EC1
SOFTWARE
LEU G:49 , VAL G:53 , PRO G:77 , TYR G:78 , TYR G:133 , TYR G:167 , ILE G:169 , ARG G:188 , HIS G:191 , HIS G:193 , FE G:1255 , HOH G:2180
BINDING SITE FOR RESIDUE BHO G1256
38
EC2
SOFTWARE
MET C:13 , LEU C:51 , LPP C:1257 , SER G:34 , TRP G:37
BINDING SITE FOR RESIDUE LPP G1257
39
EC3
SOFTWARE
LEU H:49 , ASP H:52 , VAL H:53 , ILE H:74 , GLY H:76 , PRO H:77 , TYR H:78 , TYR H:133 , TYR H:167 , ILE H:169 , ARG H:188 , HIS H:191 , HIS H:193 , GLN H:207 , FE H:1255 , HOH H:2205
BINDING SITE FOR RESIDUE BHO H1256
40
EC4
SOFTWARE
THR D:6 , MET D:13 , ILE D:17 , LPP D:1257 , ILE H:17 , ALA H:33 , SER H:34 , TRP H:37
BINDING SITE FOR RESIDUE LPP H1257
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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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
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d2boya_ (A:)
1b: SCOP_d2boyh_ (H:)
1c: SCOP_d2boyb_ (B:)
1d: SCOP_d2boyc_ (C:)
1e: SCOP_d2boyd_ (D:)
1f: SCOP_d2boye_ (E:)
1g: SCOP_d2boyf_ (F:)
1h: SCOP_d2boyg_ (G:)
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(
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)
(
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Aromatic compound dioxygenase
(111)
Family
:
automated matches
(11)
Protein domain
:
automated matches
(11)
Rhodococcus opacus [TaxId: 37919]
(11)
1a
d2boya_
A:
1b
d2boyh_
H:
1c
d2boyb_
B:
1d
d2boyc_
C:
1e
d2boyd_
D:
1f
d2boye_
E:
1g
d2boyf_
F:
1h
d2boyg_
G:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_2boyF00 (F:2-254)
1b: CATH_2boyH00 (H:2-254)
1c: CATH_2boyC00 (C:2-254)
1d: CATH_2boyD00 (D:2-254)
1e: CATH_2boyG00 (G:1-254)
1f: CATH_2boyB00 (B:2-254)
1g: CATH_2boyE00 (E:1-254)
1h: CATH_2boyA00 (A:2-254)
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Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Homologous Superfamily
:
Protocatechuate 3,4-Dioxygenase, subunit A
(43)
Rhodococcus opacus. Organism_taxid: 37919. Strain: 1cp
(2)
1a
2boyF00
F:2-254
1b
2boyH00
H:2-254
1c
2boyC00
C:2-254
1d
2boyD00
D:2-254
1e
2boyG00
G:1-254
1f
2boyB00
B:2-254
1g
2boyE00
E:1-254
1h
2boyA00
A:2-254
[
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Pfam Domains
(0, 0)
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all PFAM domains
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