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2JI3
Asym. Unit
Info
Asym.Unit (94 KB)
Biol.Unit 1 (46 KB)
Biol.Unit 2 (45 KB)
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(1)
Title
:
X-RAY STRUCTURE OF THE IRON-PEROXIDE INTERMEDIATE OF SUPEROXIDE REDUCTASE (E114A MUTANT) FROM DESULFOARCULUS BAARSII
Authors
:
G. Katona, P. Carpentier, V. Niviere, P. Amara, V. Adam, J. Ohana, N. Tsanov, D. Bourgeois
Date
:
24 Feb 07 (Deposition) - 01 May 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Oxidoreductase, Raman Spectroscopy, Superoxide Reductase, Intermediate Trapping, Microspectrophotometry, Detoxification, Electron Transport, Iron, Transport, Redox States, Metal-Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Katona, P. Carpentier, V. Niviere, P. Amara, V. Adam, J. Ohana, N. Tsanov, D. Bourgeois
Raman-Assisted Crystallography Reveals End-On Peroxide Intermediates In A Nonheme Iron Enzyme
Science V. 316 449 2007
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Hetero Components
(4, 16)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
1c: CALCIUM ION (CAc)
1d: CALCIUM ION (CAd)
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: NITRATE ION (NO3a)
4a: PEROXIDE ION (PERa)
4b: PEROXIDE ION (PERb)
4c: PEROXIDE ION (PERc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
4
Ligand/Ion
CALCIUM ION
2
FE
8
Ligand/Ion
FE (III) ION
3
NO3
1
Ligand/Ion
NITRATE ION
4
PER
3
Ligand/Ion
PEROXIDE ION
[
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Sites
(16, 16)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:10 , CYS A:13 , CYS A:29 , CYS A:30
BINDING SITE FOR RESIDUE FE A1127
02
AC2
SOFTWARE
HIS A:49 , HIS A:69 , HIS A:75 , CYS A:116 , HIS A:119 , NO3 A:1131
BINDING SITE FOR RESIDUE FE A1128
03
AC3
SOFTWARE
ASP A:33 , HOH A:2035 , HOH A:2036 , GLU C:26 , HOH C:2019 , HOH C:2029
BINDING SITE FOR RESIDUE CA A1129
04
AC4
SOFTWARE
ASP A:33 , HOH A:2026 , GLU C:26 , ASP C:33 , HOH C:2026 , HOH C:2027
BINDING SITE FOR RESIDUE CA A1130
05
AC5
SOFTWARE
LYS A:48 , HIS A:49 , HIS A:69 , PRO A:70 , HIS A:75 , HIS A:119 , FE A:1128 , HOH A:2052
BINDING SITE FOR RESIDUE NO3 A1131
06
AC6
SOFTWARE
CYS B:10 , CYS B:13 , CYS B:29 , CYS B:30
BINDING SITE FOR RESIDUE FE B1127
07
AC7
SOFTWARE
HIS B:49 , HIS B:69 , HIS B:75 , CYS B:116 , HIS B:119 , PER B:1130
BINDING SITE FOR RESIDUE FE B1128
08
AC8
SOFTWARE
HOH A:2072 , GLU B:18 , THR B:90 , HOH B:2023 , HOH B:2024 , HOH B:2075
BINDING SITE FOR RESIDUE CA B1129
09
AC9
SOFTWARE
CYS C:10 , CYS C:13 , CYS C:29 , CYS C:30
BINDING SITE FOR RESIDUE FE C1127
10
BC1
SOFTWARE
HIS C:49 , HIS C:69 , HIS C:75 , CYS C:116 , HIS C:119 , PER C:1130
BINDING SITE FOR RESIDUE FE C1128
11
BC2
SOFTWARE
GLU C:18
BINDING SITE FOR RESIDUE CA C1129
12
BC3
SOFTWARE
CYS D:10 , CYS D:13 , CYS D:29 , CYS D:30
BINDING SITE FOR RESIDUE FE D1127
13
BC4
SOFTWARE
HIS D:49 , HIS D:69 , HIS D:75 , CYS D:116 , HIS D:119 , PER D:1129
BINDING SITE FOR RESIDUE FE D1128
14
BC5
SOFTWARE
LYS B:48 , HIS B:49 , HIS B:69 , HIS B:75 , HIS B:119 , FE B:1128 , HOH B:2052 , HOH B:2087
BINDING SITE FOR RESIDUE PER B1130
15
BC6
SOFTWARE
HIS C:49 , HIS C:69 , HIS C:75 , HIS C:119 , FE C:1128
BINDING SITE FOR RESIDUE PER C1130
16
BC7
SOFTWARE
LYS D:48 , HIS D:49 , HIS D:69 , HIS D:75 , HIS D:119 , FE D:1128 , HOH D:2058 , HOH D:2059
BINDING SITE FOR RESIDUE PER D1129
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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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.
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2ji3a1 (A:38-126)
1b: SCOP_d2ji3c1 (C:38-126)
1c: SCOP_d2ji3d1 (D:38-126)
1d: SCOP_d2ji3b1 (B:38-126)
2a: SCOP_d2ji3a2 (A:1-37)
2b: SCOP_d2ji3c2 (C:1-37)
2c: SCOP_d2ji3d2 (D:2-37)
2d: SCOP_d2ji3b2 (B:2-37)
View:
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Classes
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Protein Domains
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)
(
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Organisms
(
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Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Superoxide reductase-like
(17)
Family
:
Superoxide reductase-like
(13)
Protein domain
:
automated matches
(6)
Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]
(3)
1a
d2ji3a1
A:38-126
1b
d2ji3c1
C:38-126
1c
d2ji3d1
D:38-126
1d
d2ji3b1
B:38-126
Class
:
Small proteins
(3458)
Fold
:
Rubredoxin-like
(572)
Superfamily
:
Rubredoxin-like
(127)
Family
:
automated matches
(7)
Protein domain
:
automated matches
(7)
Desulfoarculus baarsii (Desulfovibrio baarsii) [TaxId: 887]
(3)
2a
d2ji3a2
A:1-37
2b
d2ji3c2
C:1-37
2c
d2ji3d2
D:2-37
2d
d2ji3b2
B:2-37
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Desulfoferrod_N_2ji3D01 (D:2-37)
1b: PFAM_Desulfoferrod_N_2ji3D02 (D:2-37)
1c: PFAM_Desulfoferrod_N_2ji3D03 (D:2-37)
1d: PFAM_Desulfoferrod_N_2ji3D04 (D:2-37)
2a: PFAM_Desulfoferrodox_2ji3D05 (D:41-125)
2b: PFAM_Desulfoferrodox_2ji3D06 (D:41-125)
2c: PFAM_Desulfoferrodox_2ji3D07 (D:41-125)
2d: PFAM_Desulfoferrodox_2ji3D08 (D:41-125)
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Clans
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)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
Rubredoxin
(46)
Family
:
Desulfoferrod_N
(6)
Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14)
(6)
1a
Desulfoferrod_N-2ji3D01
D:2-37
1b
Desulfoferrod_N-2ji3D02
D:2-37
1c
Desulfoferrod_N-2ji3D03
D:2-37
1d
Desulfoferrod_N-2ji3D04
D:2-37
Clan
:
SOR
(12)
Family
:
Desulfoferrodox
(8)
Desulfarculus baarsii (strain ATCC 33931 / DSM 2075 / VKM B-1802 / 2st14)
(6)
2a
Desulfoferrodox-2ji3D05
D:41-125
2b
Desulfoferrodox-2ji3D06
D:41-125
2c
Desulfoferrodox-2ji3D07
D:41-125
2d
Desulfoferrodox-2ji3D08
D:41-125
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Asym.Unit (94 KB)
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