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1O9I
Asym. Unit
Info
Asym.Unit (574 KB)
Biol.Unit 1 (565 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE Y42F MUTANT OF MANGANESE CATALASE FROM LACTOBACILLUS PLANTARUM AT 1.33A RESOLUTION
Authors
:
V. V. Barynin, M. M. Whittaker, J. W. Whittaker
Date
:
13 Dec 02 (Deposition) - 18 Dec 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.33
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Oxidoreductase, Hexamer, Dimanganese Catalase, Metalloenzyme, Preoxidase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. M. Whittaker, V. V. Barynin, T. Igarashi, J. W. Whittaker
Outer Sphere Mutagenesis Of Lactobacillus Plantarum Manganese Catalase Disrupts The Cluster Core. Mechanistic Implications.
Eur. J. Biochem. V. 270 1102 2003
(for further references see the
PDB file header
)
[
close entry info
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Hetero Components
(5, 31)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
1e: CALCIUM ION (CAe)
1f: CALCIUM ION (CAf)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
2b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
2c: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESc)
2d: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESd)
2e: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESe)
3a: MANGANESE (III) ION (MN3a)
3b: MANGANESE (III) ION (MN3b)
3c: MANGANESE (III) ION (MN3c)
3d: MANGANESE (III) ION (MN3d)
3e: MANGANESE (III) ION (MN3e)
3f: MANGANESE (III) ION (MN3f)
3g: MANGANESE (III) ION (MN3g)
3h: MANGANESE (III) ION (MN3h)
3i: MANGANESE (III) ION (MN3i)
3j: MANGANESE (III) ION (MN3j)
3k: MANGANESE (III) ION (MN3k)
3l: MANGANESE (III) ION (MN3l)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: OXYGEN ATOM (Oa)
5b: OXYGEN ATOM (Ob)
5c: OXYGEN ATOM (Oc)
5d: OXYGEN ATOM (Od)
5e: OXYGEN ATOM (Oe)
5f: OXYGEN ATOM (Of)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
6
Ligand/Ion
CALCIUM ION
2
MES
5
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3
MN3
12
Ligand/Ion
MANGANESE (III) ION
4
NA
2
Ligand/Ion
SODIUM ION
5
O
6
Ligand/Ion
OXYGEN ATOM
[
close Hetero Component info
]
Sites
(31, 31)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:57 , ASP A:61 , ASN F:218 , SER F:220 , GLY F:222 , HOH F:2198
BINDING SITE FOR RESIDUE CA A 269
02
AC2
SOFTWARE
HOH A:2066 , HOH A:2102 , HOH A:2103 , LYS F:255 , GLY F:257 , HOH F:2230 , HOH F:2231
BINDING SITE FOR RESIDUE NA A 400
03
AC3
SOFTWARE
LYS D:255 , GLY D:257 , HOH D:2098 , HOH D:2227 , HOH E:2073 , HOH E:2077 , HOH E:2117
BINDING SITE FOR RESIDUE NA A 401
04
AC4
SOFTWARE
ASP B:57 , ASP B:61 , ASN C:218 , SER C:220 , GLY C:222 , HOH C:2197
BINDING SITE FOR RESIDUE CA B 269
05
AC5
SOFTWARE
ASN B:218 , SER B:220 , GLY B:222 , HOH B:2194 , ASP C:57 , ASP C:61
BINDING SITE FOR RESIDUE CA C 269
06
AC6
SOFTWARE
ASP D:57 , ASP D:61 , HOH D:2065 , ASN E:218 , SER E:220 , GLY E:222
BINDING SITE FOR RESIDUE CA D 269
07
AC7
SOFTWARE
ASN D:218 , SER D:220 , GLY D:222 , HOH D:2192 , ASP E:57 , ASP E:61
BINDING SITE FOR RESIDUE CA E 269
08
AC8
SOFTWARE
ASN A:218 , SER A:220 , GLY A:222 , ASP F:57 , ASP F:61 , HOH F:2067
BINDING SITE FOR RESIDUE CA F 269
09
AC9
SOFTWARE
GLU A:35 , GLU A:66 , HIS A:69 , MN3 A:268 , O A:270 , HOH A:2228 , HOH A:2229
BINDING SITE FOR RESIDUE MN3 A 267
10
BC1
SOFTWARE
GLU A:66 , ARG A:147 , GLU A:148 , HIS A:181 , MN3 A:267 , O A:270 , HOH A:2228
BINDING SITE FOR RESIDUE MN3 A 268
11
BC2
SOFTWARE
GLU A:66 , HIS A:69 , GLU A:148 , HIS A:181 , MN3 A:267 , MN3 A:268 , HOH A:2228 , HOH A:2229
BINDING SITE FOR RESIDUE O A 270
12
BC3
SOFTWARE
PRO A:259 , HOH A:2230 , HOH A:2231 , HOH A:2232 , HOH D:2177 , GLU F:89
BINDING SITE FOR RESIDUE MES A 273
13
BC4
SOFTWARE
GLU B:35 , GLU B:66 , HIS B:69 , MN3 B:268 , O B:270 , HOH B:2241 , HOH B:2242
BINDING SITE FOR RESIDUE MN3 B 267
14
BC5
SOFTWARE
GLU B:66 , ARG B:147 , GLU B:148 , HIS B:181 , MN3 B:267 , O B:270 , HOH B:2241
BINDING SITE FOR RESIDUE MN3 B 268
15
BC6
SOFTWARE
GLU B:66 , HIS B:69 , HIS B:181 , MN3 B:267 , MN3 B:268 , HOH B:2241 , HOH B:2242
BINDING SITE FOR RESIDUE O B 270
16
BC7
SOFTWARE
GLU C:35 , GLU C:66 , HIS C:69 , MN3 C:268 , O C:270 , HOH C:2241 , HOH C:2242
BINDING SITE FOR RESIDUE MN3 C 267
17
BC8
SOFTWARE
GLU C:66 , ARG C:147 , GLU C:148 , HIS C:181 , MN3 C:267 , O C:270 , HOH C:2241
BINDING SITE FOR RESIDUE MN3 C 268
18
BC9
SOFTWARE
GLU C:66 , HIS C:69 , GLU C:148 , HIS C:181 , MN3 C:267 , MN3 C:268 , HOH C:2241 , HOH C:2242
BINDING SITE FOR RESIDUE O C 270
19
CC1
SOFTWARE
GLU D:35 , GLU D:66 , HIS D:69 , MN3 D:268 , O D:270 , HOH D:2242 , HOH D:2243
BINDING SITE FOR RESIDUE MN3 D 267
20
CC2
SOFTWARE
GLU D:66 , ARG D:147 , GLU D:148 , HIS D:181 , MN3 D:267 , O D:270 , HOH D:2243
BINDING SITE FOR RESIDUE MN3 D 268
21
CC3
SOFTWARE
GLU D:66 , HIS D:69 , GLU D:148 , HIS D:181 , MN3 D:267 , MN3 D:268 , HOH D:2242 , HOH D:2243
BINDING SITE FOR RESIDUE O D 270
22
CC4
SOFTWARE
GLU E:35 , GLU E:66 , HIS E:69 , MN3 E:268 , O E:270 , HOH E:2245 , HOH E:2246
BINDING SITE FOR RESIDUE MN3 E 267
23
CC5
SOFTWARE
GLU E:66 , ARG E:147 , GLU E:148 , HIS E:181 , MN3 E:267 , O E:270 , HOH E:2245
BINDING SITE FOR RESIDUE MN3 E 268
24
CC6
SOFTWARE
GLU E:66 , HIS E:69 , GLU E:148 , HIS E:181 , MN3 E:267 , MN3 E:268 , HOH E:2245 , HOH E:2246
BINDING SITE FOR RESIDUE O E 270
25
CC7
SOFTWARE
HOH A:2134 , LYS E:92 , PRO E:259 , HOH E:2247 , HOH E:2248 , HOH F:2181
BINDING SITE FOR RESIDUE MES E 273
26
CC8
SOFTWARE
PRO D:14 , ARG D:16 , SER D:17 , TYR D:79 , GLU D:82 , ARG E:16 , SER E:17 , LYS E:255
BINDING SITE FOR RESIDUE MES E 274
27
CC9
SOFTWARE
GLU F:35 , GLU F:66 , HIS F:69 , MN3 F:268 , O F:270 , HOH F:2248 , HOH F:2249
BINDING SITE FOR RESIDUE MN3 F 267
28
DC1
SOFTWARE
GLU F:66 , ARG F:147 , GLU F:148 , HIS F:181 , MN3 F:267 , O F:270 , HOH F:2249
BINDING SITE FOR RESIDUE MN3 F 268
29
DC2
SOFTWARE
GLU F:66 , HIS F:69 , GLU F:148 , HIS F:181 , MN3 F:267 , MN3 F:268 , HOH F:2248 , HOH F:2249
BINDING SITE FOR RESIDUE O F 270
30
DC3
SOFTWARE
GLY A:250 , ILE A:251 , LYS F:7 , HOH F:2250
BINDING SITE FOR RESIDUE MES F 273
31
DC4
SOFTWARE
GLU B:89 , ARG C:260 , SER F:160 , ARG F:168 , HOH F:2143 , HOH F:2251
BINDING SITE FOR RESIDUE MES F 274
[
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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
;
View:
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Label:
End label:
Sorry, no Info available
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1o9ia_ (A:)
1b: SCOP_d1o9ib_ (B:)
1c: SCOP_d1o9ic_ (C:)
1d: SCOP_d1o9id_ (D:)
1e: SCOP_d1o9ie_ (E:)
1f: SCOP_d1o9if_ (F:)
View:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Ferritin-like
(533)
Superfamily
:
Ferritin-like
(489)
Family
:
Manganese catalase (T-catalase)
(7)
Protein domain
:
Manganese catalase (T-catalase)
(4)
Lactobacillus plantarum [TaxId: 1590]
(3)
1a
d1o9ia_
A:
1b
d1o9ib_
B:
1c
d1o9ic_
C:
1d
d1o9id_
D:
1e
d1o9ie_
E:
1f
d1o9if_
F:
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1o9iA02 (A:204-266)
1b: CATH_1o9iB02 (B:204-266)
1c: CATH_1o9iC02 (C:204-266)
1d: CATH_1o9iD02 (D:204-266)
1e: CATH_1o9iE02 (E:204-266)
1f: CATH_1o9iF02 (F:204-266)
2a: CATH_1o9iA01 (A:1-203)
2b: CATH_1o9iB01 (B:1-203)
2c: CATH_1o9iC01 (C:1-203)
2d: CATH_1o9iD01 (D:1-203)
2e: CATH_1o9iE01 (E:1-203)
2f: CATH_1o9iF01 (F:1-203)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
manganese catalase, domain 2, chain A
(3)
Homologous Superfamily
:
manganese catalase, domain 2, chain A
(3)
Lactobacillus plantarum. Organism_taxid: 1590.
(1)
1a
1o9iA02
A:204-266
1b
1o9iB02
B:204-266
1c
1o9iC02
C:204-266
1d
1o9iD02
D:204-266
1e
1o9iE02
E:204-266
1f
1o9iF02
F:204-266
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Ferritin;
(180)
Homologous Superfamily
:
[code=1.20.1260.10, no name defined]
(180)
Lactobacillus plantarum. Organism_taxid: 1590.
(1)
2a
1o9iA01
A:1-203
2b
1o9iB01
B:1-203
2c
1o9iC01
C:1-203
2d
1o9iD01
D:1-203
2e
1o9iE01
E:1-203
2f
1o9iF01
F:1-203
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Chain F
Asymmetric Unit 1
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Asym.Unit (574 KB)
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