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1XDC
Asym. Unit
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Asym.Unit (80 KB)
Biol.Unit 1 (145 KB)
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(1)
Title
:
HYDROGEN BONDING IN HUMAN MANGANESE SUPEROXIDE DISMUTASE CONTAINING 3-FLUOROTYROSINE
Authors
:
I. Ayala, J. J. Perry, J. Szczepanski, D. E. Cabelli, J. A. Tainer, M. T. V H. S. Nick, D. N. Silverman
Date
:
05 Sep 04 (Deposition) - 22 Mar 05 (Release) - 16 Nov 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Mnsod, Manganese Superoxide Dismutase, 3-Fluorotyrosine, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
I. Ayala, J. J. Perry, J. Szczepanski, J. A. Tainer, M. T. Vala, H. S. Nick, D. N. Silverman
Hydrogen Bonding In Human Manganese Superoxide Dismutase Containing 3-Fluorotyrosine
Biophys. J. V. 89 4171 2005
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Hetero Components
(2, 20)
Info
All Hetero Components
1a: MANGANESE (II) ION (MNa)
1b: MANGANESE (II) ION (MNb)
2a: 3-FLUOROTYROSINE (YOFa)
2b: 3-FLUOROTYROSINE (YOFb)
2c: 3-FLUOROTYROSINE (YOFc)
2d: 3-FLUOROTYROSINE (YOFd)
2e: 3-FLUOROTYROSINE (YOFe)
2f: 3-FLUOROTYROSINE (YOFf)
2g: 3-FLUOROTYROSINE (YOFg)
2h: 3-FLUOROTYROSINE (YOFh)
2i: 3-FLUOROTYROSINE (YOFi)
2j: 3-FLUOROTYROSINE (YOFj)
2k: 3-FLUOROTYROSINE (YOFk)
2l: 3-FLUOROTYROSINE (YOFl)
2m: 3-FLUOROTYROSINE (YOFm)
2n: 3-FLUOROTYROSINE (YOFn)
2o: 3-FLUOROTYROSINE (YOFo)
2p: 3-FLUOROTYROSINE (YOFp)
2q: 3-FLUOROTYROSINE (YOFq)
2r: 3-FLUOROTYROSINE (YOFr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MN
2
Ligand/Ion
MANGANESE (II) ION
2
YOF
18
Mod. Amino Acid
3-FLUOROTYROSINE
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Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:26 , HIS A:74 , ASP A:159 , HIS A:163 , HOH A:697
BINDING SITE FOR RESIDUE MN A 500
2
AC2
SOFTWARE
HIS B:26 , HIS B:74 , ASP B:159 , HIS B:163 , HOH B:852
BINDING SITE FOR RESIDUE MN B 600
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_019364 (E42V, chain A/B, )
2: VAR_025898 (G52R, chain A/B, )
3: VAR_007165 (I58T, chain A/B, )
4: VAR_019365 (R132W, chain A/B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_019364
E
66
V
SODM_HUMAN
Polymorphism
5746097
A/B
E
42
V
2
UniProt
VAR_025898
G
76
R
SODM_HUMAN
Polymorphism
4987023
A/B
G
52
R
3
UniProt
VAR_007165
I
82
T
SODM_HUMAN
Polymorphism
1141718
A/B
I
58
T
4
UniProt
VAR_019365
R
156
W
SODM_HUMAN
Polymorphism
5746129
A/B
R
132
W
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: SOD_MN (A:159-166,B:159-166)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
SOD_MN
PS00088
Manganese and iron superoxide dismutases signature.
SODM_HUMAN
183-190
2
A:159-166
B:159-166
[
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Exons
(4, 8)
Info
All Exons
Exon 1.2a (A:1-52 | B:1-52)
Exon 1.3 (A:52-91 | B:52-91)
Exon 1.4 (A:91-151 | B:91-151)
Exon 1.5a (A:151-198 | B:151-198)
View:
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All Exon Boundaries
1: Boundary 1.1b/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5a
5: Boundary 1.5a/1.6b
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000367055
1b
ENSE00001872926
chr6:
160114352-160114177
176
SODM_HUMAN
1-8
8
0
-
-
1.2a
ENST00000367055
2a
ENSE00000815316
chr6:
160113895-160113693
203
SODM_HUMAN
8-76
69
2
A:1-52
B:1-52
52
52
1.3
ENST00000367055
3
ENSE00000765625
chr6:
160109274-160109158
117
SODM_HUMAN
76-115
40
2
A:52-91
B:52-91
40
40
1.4
ENST00000367055
4
ENSE00000765624
chr6:
160106065-160105886
180
SODM_HUMAN
115-175
61
2
A:91-151
B:91-151
61
61
1.5a
ENST00000367055
5a
ENSE00001431742
chr6:
160103670-160103506
165
SODM_HUMAN
175-222
48
2
A:151-198
B:151-198
48
48
1.6b
ENST00000367055
6b
ENSE00001926068
chr6:
160100330-160100148
183
SODM_HUMAN
-
0
0
-
-
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1xdca1 (A:1-83)
1b: SCOP_d1xdcb1 (B:1-83)
2a: SCOP_d1xdca2 (A:84-198)
2b: SCOP_d1xdcb2 (B:84-198)
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Protein Domains
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Organisms
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(
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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
:
Mn superoxide dismutase (MnSOD)
(47)
Human (Homo sapiens) [TaxId: 9606]
(26)
1a
d1xdca1
A:1-83
1b
d1xdcb1
B:1-83
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
:
Mn superoxide dismutase (MnSOD)
(47)
Human (Homo sapiens) [TaxId: 9606]
(26)
2a
d1xdca2
A:84-198
2b
d1xdcb2
B:84-198
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Sod_Fe_C_1xdcB01 (B:87-193)
1b: PFAM_Sod_Fe_C_1xdcB02 (B:87-193)
2a: PFAM_Sod_Fe_N_1xdcB03 (B:1-82)
2b: PFAM_Sod_Fe_N_1xdcB04 (B:1-82)
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)
Clan
:
no clan defined [family: Sod_Fe_C]
(46)
Family
:
Sod_Fe_C
(46)
Homo sapiens (Human)
(17)
1a
Sod_Fe_C-1xdcB01
B:87-193
1b
Sod_Fe_C-1xdcB02
B:87-193
Clan
:
no clan defined [family: Sod_Fe_N]
(46)
Family
:
Sod_Fe_N
(46)
Homo sapiens (Human)
(17)
2a
Sod_Fe_N-1xdcB03
B:1-82
2b
Sod_Fe_N-1xdcB04
B:1-82
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