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2NYB
Biol. Unit 2
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Asym.Unit (306 KB)
Biol.Unit 1 (154 KB)
Biol.Unit 2 (150 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF E.COLI IRON SUPEROXIDE DISMUTASE Q69E AT 1.1 ANGSTROM RESOLUTION
Authors
:
J. C. Porta, A. Vahedi-Faridi, G. E. O. Borgstahl
Date
:
20 Nov 06 (Deposition) - 05 Dec 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Iron Superoxide Dismutase Q69E, Fesod, Oxidoreductase
(Keyword Search:
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Reference
:
E. Yikilmaz, J. Porta, L. E. Grove, A. Vahedi-Faridi, Y. Bronshteyn, T. C. Brunold, G. E. Borgstahl, A. F. Miller
How Can A Single Second Sphere Amino Acid Substitution Cause Reduction Midpoint Potential Changes Of Hundreds Of Millivolts?
J. Am. Chem. Soc. V. 129 9927 2007
(for further references see the
PDB file header
)
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: FE (II) ION (FE2a)
1b: FE (II) ION (FE2b)
1c: FE (II) ION (FE2c)
1d: FE (II) ION (FE2d)
2a: OXYGEN ATOM (Oa)
2b: OXYGEN ATOM (Ob)
2c: OXYGEN ATOM (Oc)
2d: OXYGEN ATOM (Od)
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Label:
No.
Name
Count
Type
Full Name
1
FE2
2
Ligand/Ion
FE (II) ION
2
O
-1
Ligand/Ion
OXYGEN ATOM
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Sites
(4, 4)
Info
All Sites
1: AC3 (SOFTWARE)
2: AC4 (SOFTWARE)
3: AC7 (SOFTWARE)
4: AC8 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
AC3
SOFTWARE
HIS C:26 , HIS C:73 , ASP C:156 , HIS C:160 , O C:194
BINDING SITE FOR RESIDUE FE2 C 193
2
AC4
SOFTWARE
HIS D:26 , HIS D:73 , ASP D:156 , HIS D:160 , O D:194
BINDING SITE FOR RESIDUE FE2 D 193
3
AC7
SOFTWARE
GLU C:69 , HIS C:73 , TRP C:122 , ASP C:156 , TRP C:158 , HIS C:160 , FE2 C:193
BINDING SITE FOR RESIDUE O C 194
4
AC8
SOFTWARE
GLU D:69 , HIS D:73 , TRP D:122 , ASP D:156 , TRP D:158 , HIS D:160 , FE2 D:193
BINDING SITE FOR RESIDUE O D 194
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SOD_MN (C:156-163,D:156-163)
;
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PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_MN
PS00088
Manganese and iron superoxide dismutases signature.
SODF_ECOLI
157-164
2
-
-
C:156-163
D:156-163
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Exons
(0, 0)
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2nyba1 (A:1-82)
1b: SCOP_d2nybb1 (B:1-82)
1c: SCOP_d2nybc1 (C:1-82)
1d: SCOP_d2nybd1 (D:1-82)
2a: SCOP_d2nyba2 (A:83-192)
2b: SCOP_d2nybb2 (B:83-192)
2c: SCOP_d2nybc2 (C:83-192)
2d: SCOP_d2nybd2 (D:83-192)
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Protein Domains
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)
(
)
Organisms
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)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Long alpha-hairpin
(315)
Superfamily
:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
(122)
Family
:
Fe,Mn superoxide dismutase (SOD), N-terminal domain
(80)
Protein domain
:
Fe superoxide dismutase (FeSOD)
(21)
Escherichia coli [TaxId: 562]
(5)
1a
d2nyba1
A:1-82
1b
d2nybb1
B:1-82
1c
d2nybc1
C:1-82
1d
d2nybd1
D:1-82
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Fe,Mn superoxide dismutase (SOD), C-terminal domain
(122)
Superfamily
:
Fe,Mn superoxide dismutase (SOD), C-terminal domain
(122)
Family
:
Fe,Mn superoxide dismutase (SOD), C-terminal domain
(82)
Protein domain
:
Fe superoxide dismutase (FeSOD)
(21)
Escherichia coli [TaxId: 562]
(5)
2a
d2nyba2
A:83-192
2b
d2nybb2
B:83-192
2c
d2nybc2
C:83-192
2d
d2nybd2
D:83-192
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CATH Domains
(0, 0)
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Sod_Fe_C_2nybD01 (D:86-190)
1b: PFAM_Sod_Fe_C_2nybD02 (D:86-190)
1c: PFAM_Sod_Fe_C_2nybD03 (D:86-190)
1d: PFAM_Sod_Fe_C_2nybD04 (D:86-190)
2a: PFAM_Sod_Fe_N_2nybD05 (D:1-81)
2b: PFAM_Sod_Fe_N_2nybD06 (D:1-81)
2c: PFAM_Sod_Fe_N_2nybD07 (D:1-81)
2d: PFAM_Sod_Fe_N_2nybD08 (D:1-81)
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Clan
:
no clan defined [family: Sod_Fe_C]
(46)
Family
:
Sod_Fe_C
(46)
Escherichia coli (strain K12)
(7)
1a
Sod_Fe_C-2nybD01
D:86-190
1b
Sod_Fe_C-2nybD02
D:86-190
1c
Sod_Fe_C-2nybD03
D:86-190
1d
Sod_Fe_C-2nybD04
D:86-190
Clan
:
no clan defined [family: Sod_Fe_N]
(46)
Family
:
Sod_Fe_N
(46)
Escherichia coli (strain K12)
(7)
2a
Sod_Fe_N-2nybD05
D:1-81
2b
Sod_Fe_N-2nybD06
D:1-81
2c
Sod_Fe_N-2nybD07
D:1-81
2d
Sod_Fe_N-2nybD08
D:1-81
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Asymmetric Unit 1
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Asym.Unit (306 KB)
Header - Asym.Unit
Biol.Unit 1 (154 KB)
Header - Biol.Unit 1
Biol.Unit 2 (150 KB)
Header - Biol.Unit 2
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