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2JI3
Biol. Unit 2
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:
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Gene Ontology, PubMed, Web (Google)
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)
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
(1, 2)
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:
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Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
FE
-1
Ligand/Ion
FE (III) ION
3
NO3
-1
Ligand/Ion
NITRATE ION
4
PER
2
Ligand/Ion
PEROXIDE ION
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Sites
(9, 9)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC9 (SOFTWARE)
4: BC1 (SOFTWARE)
5: BC2 (SOFTWARE)
6: BC3 (SOFTWARE)
7: BC4 (SOFTWARE)
8: BC6 (SOFTWARE)
9: BC7 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
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
2
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
3
AC9
SOFTWARE
CYS C:10 , CYS C:13 , CYS C:29 , CYS C:30
BINDING SITE FOR RESIDUE FE C1127
4
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
5
BC2
SOFTWARE
GLU C:18
BINDING SITE FOR RESIDUE CA C1129
6
BC3
SOFTWARE
CYS D:10 , CYS D:13 , CYS D:29 , CYS D:30
BINDING SITE FOR RESIDUE FE D1127
7
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
8
BC6
SOFTWARE
HIS C:49 , HIS C:69 , HIS C:75 , HIS C:119 , FE C:1128
BINDING SITE FOR RESIDUE PER C1130
9
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 only available for the asymmetric unit)
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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
(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)
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Protein Domains
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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)
Info
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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)
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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Asymmetric Unit 1
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Asym.Unit (94 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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