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Zinc in PDB 1n18: Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S

Enzymatic activity of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S

All present enzymatic activity of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S:
1.15.1.1;

Protein crystallography data

The structure of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S, PDB code: 1n18 was solved by R.M.F.Cardoso, M.M.Thayer, M.Didonato, T.P.Lo, C.K.Bruns, E.D.Getzoff, J.A.Tainer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.86 / 2.00
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 203.200, 165.200, 144.300, 90.00, 90.00, 90.00
R / Rfree (%) 21.8 / 25

Other elements in 1n18:

The structure of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S also contains other interesting chemical elements:

Copper (Cu) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S (pdb code 1n18). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S, PDB code: 1n18:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 1n18

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Zinc binding site 1 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:33.1
occ:1.00
OD1 A:ASP83 1.9 26.7 1.0
ND1 A:HIS63 2.0 28.5 1.0
ND1 A:HIS71 2.0 40.0 1.0
ND1 A:HIS80 2.1 32.1 1.0
CG A:ASP83 2.7 30.2 1.0
OD2 A:ASP83 2.9 31.6 1.0
CE1 A:HIS71 2.9 40.0 1.0
CE1 A:HIS80 3.0 32.9 1.0
CE1 A:HIS63 3.0 28.0 1.0
CG A:HIS63 3.0 27.3 1.0
CG A:HIS80 3.1 33.7 1.0
CG A:HIS71 3.1 39.3 1.0
CB A:HIS63 3.3 25.2 1.0
CB A:HIS80 3.5 33.5 1.0
CB A:HIS71 3.5 39.2 1.0
O A:LYS136 3.8 42.4 1.0
CA A:HIS71 3.9 39.3 1.0
NE2 A:HIS71 4.1 39.6 1.0
NE2 A:HIS80 4.1 31.9 1.0
NE2 A:HIS63 4.1 31.0 1.0
CD2 A:HIS63 4.1 28.4 1.0
CB A:ASP83 4.1 27.7 1.0
CD2 A:HIS80 4.2 31.5 1.0
CD2 A:HIS71 4.2 39.7 1.0
N A:GLY72 4.7 37.8 1.0
CA A:ASP83 4.7 29.3 1.0
O A:HOH203 4.7 29.8 1.0
CA A:HIS80 4.7 35.6 1.0
N A:HIS80 4.8 37.4 1.0
C A:HIS71 4.8 38.3 1.0
C A:LYS136 4.8 43.4 1.0
CA A:HIS63 4.9 24.9 1.0
N A:ASP83 4.9 28.9 1.0
N A:HIS71 4.9 38.6 1.0

Zinc binding site 2 out of 10 in 1n18

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Zinc binding site 2 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:22.6
occ:1.00
OD1 B:ASP83 2.0 21.5 1.0
ND1 B:HIS63 2.0 19.6 1.0
ND1 B:HIS71 2.0 17.7 1.0
ND1 B:HIS80 2.1 22.8 1.0
CG B:ASP83 2.8 23.9 1.0
CE1 B:HIS71 2.9 20.8 1.0
CE1 B:HIS63 2.9 19.5 1.0
OD2 B:ASP83 3.0 22.6 1.0
CE1 B:HIS80 3.0 23.2 1.0
CG B:HIS63 3.1 21.3 1.0
CG B:HIS80 3.1 21.4 1.0
CG B:HIS71 3.1 21.6 1.0
CB B:HIS63 3.5 22.1 1.0
CB B:HIS80 3.5 20.4 1.0
CB B:HIS71 3.6 21.6 1.0
O B:LYS136 3.9 26.9 1.0
CA B:HIS71 3.9 22.4 1.0
NE2 B:HIS71 4.0 18.1 1.0
NE2 B:HIS63 4.1 22.1 1.0
NE2 B:HIS80 4.1 21.2 1.0
CD2 B:HIS63 4.2 21.0 1.0
CD2 B:HIS80 4.2 21.5 1.0
CD2 B:HIS71 4.2 19.6 1.0
CB B:ASP83 4.2 20.9 1.0
CA B:ASP83 4.7 19.6 1.0
O B:HOH188 4.7 25.5 1.0
N B:GLY72 4.7 19.8 1.0
N B:HIS80 4.8 21.5 1.0
CA B:HIS80 4.8 21.2 1.0
C B:LYS136 4.8 26.6 1.0
C B:HIS71 4.9 22.2 1.0
N B:ASP83 4.9 19.3 1.0
N B:HIS71 5.0 21.9 1.0
CA B:HIS63 5.0 23.6 1.0

Zinc binding site 3 out of 10 in 1n18

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Zinc binding site 3 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:41.4
occ:1.00
OD1 C:ASP83 1.8 39.0 1.0
ND1 C:HIS71 2.1 41.4 1.0
ND1 C:HIS80 2.1 31.9 1.0
ND1 C:HIS63 2.4 44.5 1.0
CG C:ASP83 2.6 35.5 1.0
CE1 C:HIS71 2.8 41.9 1.0
OD2 C:ASP83 2.9 34.7 1.0
CG C:HIS80 3.0 36.9 1.0
CE1 C:HIS80 3.0 32.4 1.0
CG C:HIS71 3.2 41.5 1.0
CG C:HIS63 3.2 44.5 1.0
CB C:HIS80 3.4 34.9 1.0
CE1 C:HIS63 3.4 47.1 1.0
CB C:HIS63 3.4 41.7 1.0
CB C:HIS71 3.7 41.5 1.0
CA C:HIS71 4.0 43.4 1.0
NE2 C:HIS71 4.0 41.1 1.0
O C:LYS136 4.1 46.9 1.0
CB C:ASP83 4.1 35.0 1.0
NE2 C:HIS80 4.1 34.7 1.0
CD2 C:HIS80 4.1 34.5 1.0
CD2 C:HIS71 4.2 41.1 1.0
CD2 C:HIS63 4.4 47.0 1.0
NE2 C:HIS63 4.4 47.0 1.0
N C:GLY72 4.6 42.4 1.0
CA C:ASP83 4.6 34.2 1.0
CA C:HIS80 4.6 36.5 1.0
N C:HIS80 4.7 39.9 1.0
N C:ASP83 4.8 35.2 1.0
C C:HIS71 4.9 43.5 1.0
CA C:HIS63 5.0 38.4 1.0

Zinc binding site 4 out of 10 in 1n18

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Zinc binding site 4 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:22.5
occ:1.00
OD1 D:ASP83 1.9 20.3 1.0
ND1 D:HIS63 2.0 23.1 1.0
ND1 D:HIS71 2.0 20.5 1.0
ND1 D:HIS80 2.0 22.8 1.0
CG D:ASP83 2.7 18.1 1.0
CE1 D:HIS71 2.8 19.7 1.0
OD2 D:ASP83 2.8 19.0 1.0
CE1 D:HIS63 2.9 23.9 1.0
CE1 D:HIS80 2.9 22.5 1.0
CG D:HIS63 3.0 24.4 1.0
CG D:HIS80 3.0 22.1 1.0
CG D:HIS71 3.1 22.0 1.0
CB D:HIS63 3.4 23.3 1.0
CB D:HIS80 3.5 22.2 1.0
CB D:HIS71 3.6 22.8 1.0
O D:LYS136 3.8 25.2 1.0
CA D:HIS71 4.0 23.9 1.0
NE2 D:HIS71 4.0 19.6 1.0
NE2 D:HIS63 4.0 27.1 1.0
NE2 D:HIS80 4.0 23.3 1.0
CD2 D:HIS63 4.1 25.1 1.0
CD2 D:HIS80 4.1 21.9 1.0
CB D:ASP83 4.1 19.6 1.0
CD2 D:HIS71 4.2 19.3 1.0
CA D:ASP83 4.7 20.7 1.0
CA D:HIS80 4.7 23.0 1.0
N D:GLY72 4.7 23.9 1.0
N D:HIS80 4.8 22.9 1.0
C D:LYS136 4.8 24.7 1.0
O D:HOH1442 4.8 27.2 1.0
N D:ASP83 4.9 21.0 1.0
C D:HIS71 4.9 24.3 1.0
CA D:HIS63 5.0 24.2 1.0

Zinc binding site 5 out of 10 in 1n18

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Zinc binding site 5 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn155

b:24.3
occ:1.00
OD1 E:ASP83 1.9 21.7 1.0
ND1 E:HIS80 2.0 24.8 1.0
ND1 E:HIS63 2.1 22.9 1.0
ND1 E:HIS71 2.1 26.6 1.0
CG E:ASP83 2.8 23.0 1.0
CE1 E:HIS80 2.9 25.6 1.0
CE1 E:HIS71 3.0 25.4 1.0
CG E:HIS80 3.0 25.6 1.0
OD2 E:ASP83 3.0 22.1 1.0
CG E:HIS63 3.0 22.1 1.0
CE1 E:HIS63 3.0 18.5 1.0
CG E:HIS71 3.2 25.3 1.0
CB E:HIS63 3.4 20.4 1.0
CB E:HIS80 3.4 24.4 1.0
CB E:HIS71 3.6 25.9 1.0
O E:LYS136 3.7 27.6 1.0
CA E:HIS71 4.0 26.9 1.0
NE2 E:HIS80 4.0 24.8 1.0
CD2 E:HIS80 4.1 25.0 1.0
NE2 E:HIS71 4.1 25.7 1.0
NE2 E:HIS63 4.2 23.1 1.0
CB E:ASP83 4.2 21.1 1.0
CD2 E:HIS63 4.2 21.3 1.0
CD2 E:HIS71 4.3 25.2 1.0
CA E:ASP83 4.6 22.8 1.0
CA E:HIS80 4.7 24.7 1.0
N E:HIS80 4.7 26.1 1.0
O E:HOH159 4.7 22.7 1.0
C E:LYS136 4.8 28.7 1.0
N E:GLY72 4.8 25.1 1.0
N E:ASP83 4.8 22.2 1.0
CA E:HIS63 4.9 22.1 1.0
C E:HIS71 4.9 26.3 1.0
N E:HIS71 5.0 27.9 1.0

Zinc binding site 6 out of 10 in 1n18

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Zinc binding site 6 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:22.9
occ:1.00
OD1 F:ASP83 1.9 21.0 1.0
ND1 F:HIS80 2.1 21.4 1.0
ND1 F:HIS63 2.1 21.4 1.0
ND1 F:HIS71 2.1 22.0 1.0
CG F:ASP83 2.8 22.0 1.0
OD2 F:ASP83 2.9 23.2 1.0
CE1 F:HIS71 2.9 21.2 1.0
CE1 F:HIS80 3.0 24.2 1.0
CG F:HIS80 3.0 22.6 1.0
CE1 F:HIS63 3.0 20.1 1.0
CG F:HIS63 3.1 21.8 1.0
CG F:HIS71 3.2 19.9 1.0
CB F:HIS63 3.4 22.8 1.0
CB F:HIS80 3.4 21.5 1.0
CB F:HIS71 3.6 20.4 1.0
O F:LYS136 3.9 27.9 1.0
CA F:HIS71 4.0 25.2 1.0
NE2 F:HIS80 4.1 23.4 1.0
CD2 F:HIS80 4.1 23.1 1.0
NE2 F:HIS71 4.1 20.2 1.0
NE2 F:HIS63 4.1 26.2 1.0
CB F:ASP83 4.2 20.6 1.0
CD2 F:HIS63 4.2 23.9 1.0
CD2 F:HIS71 4.3 19.0 1.0
CA F:HIS80 4.7 23.2 1.0
N F:HIS80 4.7 24.0 1.0
CA F:ASP83 4.7 20.4 1.0
N F:GLY72 4.7 25.4 1.0
O F:HOH179 4.9 26.8 1.0
C F:LYS136 4.9 26.9 1.0
N F:ASP83 4.9 20.3 1.0
C F:HIS71 4.9 26.1 1.0
CA F:HIS63 4.9 22.2 1.0
CD2 F:HIS46 5.0 20.1 1.0
N F:HIS71 5.0 27.2 1.0

Zinc binding site 7 out of 10 in 1n18

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Zinc binding site 7 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn155

b:45.8
occ:1.00
OD1 G:ASP83 1.9 42.0 1.0
ND1 G:HIS80 2.1 47.4 1.0
ND1 G:HIS71 2.1 52.1 1.0
ND1 G:HIS63 2.2 43.9 1.0
CG G:ASP83 2.7 42.2 1.0
OD2 G:ASP83 2.9 38.8 1.0
CE1 G:HIS80 2.9 48.6 1.0
CG G:HIS80 3.0 49.4 1.0
CE1 G:HIS71 3.0 53.5 1.0
CG G:HIS63 3.1 43.8 1.0
CE1 G:HIS63 3.2 46.3 1.0
CG G:HIS71 3.2 53.0 1.0
CB G:HIS63 3.4 41.4 1.0
CB G:HIS80 3.4 49.1 1.0
CB G:HIS71 3.6 53.9 1.0
CA G:HIS71 3.8 55.6 1.0
O G:LYS136 3.9 56.5 1.0
NE2 G:HIS80 4.0 49.8 1.0
CD2 G:HIS80 4.0 49.2 1.0
CB G:ASP83 4.2 42.0 1.0
NE2 G:HIS71 4.2 54.0 1.0
CD2 G:HIS63 4.3 45.5 1.0
NE2 G:HIS63 4.3 48.5 1.0
CD2 G:HIS71 4.3 52.8 1.0
N G:GLY72 4.6 55.2 1.0
N G:HIS80 4.7 50.5 1.0
CA G:HIS80 4.7 48.8 1.0
CA G:ASP83 4.7 41.9 1.0
C G:HIS71 4.8 55.7 1.0
N G:HIS71 4.8 57.0 1.0
N G:ASP83 4.8 41.7 1.0
CD2 G:HIS46 4.8 46.8 1.0
C G:LYS136 4.9 56.4 1.0
CA G:HIS63 4.9 39.1 1.0
O G:HOH245 5.0 48.8 1.0

Zinc binding site 8 out of 10 in 1n18

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Zinc binding site 8 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn155

b:28.7
occ:1.00
OD1 H:ASP83 1.9 27.1 1.0
ND1 H:HIS63 2.0 31.3 1.0
ND1 H:HIS71 2.1 25.4 1.0
ND1 H:HIS80 2.1 34.3 1.0
CG H:ASP83 2.7 28.5 1.0
OD2 H:ASP83 2.9 26.9 1.0
CE1 H:HIS80 2.9 34.9 1.0
CE1 H:HIS71 2.9 25.4 1.0
CE1 H:HIS63 3.0 31.0 1.0
CG H:HIS80 3.0 33.0 1.0
CG H:HIS63 3.0 30.5 1.0
CG H:HIS71 3.1 28.8 1.0
CB H:HIS63 3.4 30.7 1.0
CB H:HIS80 3.4 31.7 1.0
CB H:HIS71 3.6 29.0 1.0
NE2 H:HIS80 3.9 35.9 1.0
CA H:HIS71 4.0 30.7 1.0
CD2 H:HIS80 4.0 33.8 1.0
O H:LYS136 4.0 34.6 1.0
NE2 H:HIS63 4.1 32.6 1.0
NE2 H:HIS71 4.1 26.1 1.0
CB H:ASP83 4.1 27.0 1.0
CD2 H:HIS63 4.1 31.3 1.0
CD2 H:HIS71 4.2 27.7 1.0
N H:HIS80 4.6 31.8 1.0
CA H:ASP83 4.6 27.0 1.0
CA H:HIS80 4.6 30.9 1.0
N H:GLY72 4.8 31.0 1.0
N H:ASP83 4.8 27.6 1.0
O H:HOH172 4.9 33.3 1.0
CA H:HIS63 4.9 32.2 1.0
N H:HIS71 4.9 33.5 1.0
C H:HIS71 4.9 32.5 1.0
C H:LYS136 5.0 34.7 1.0

Zinc binding site 9 out of 10 in 1n18

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Zinc binding site 9 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn155

b:40.5
occ:1.00
ND1 I:HIS71 2.0 47.7 1.0
OD1 I:ASP83 2.0 41.7 1.0
ND1 I:HIS63 2.1 39.7 1.0
ND1 I:HIS80 2.1 40.9 1.0
CE1 I:HIS71 2.7 48.4 1.0
CG I:ASP83 2.8 41.3 1.0
CE1 I:HIS80 2.9 40.7 1.0
OD2 I:ASP83 3.0 43.8 1.0
CE1 I:HIS63 3.1 39.3 1.0
CG I:HIS80 3.1 41.5 1.0
CG I:HIS63 3.1 40.1 1.0
CG I:HIS71 3.1 48.3 1.0
CB I:HIS63 3.4 41.0 1.0
CB I:HIS80 3.6 42.2 1.0
CB I:HIS71 3.7 47.4 1.0
NE2 I:HIS71 3.9 47.8 1.0
NE2 I:HIS80 4.0 42.0 1.0
O I:LYS136 4.0 49.2 1.0
CD2 I:HIS80 4.1 41.0 1.0
CA I:HIS71 4.1 48.0 1.0
CD2 I:HIS71 4.1 48.0 1.0
NE2 I:HIS63 4.2 40.0 1.0
CD2 I:HIS63 4.2 39.1 1.0
CB I:ASP83 4.2 39.1 1.0
CD2 I:HIS46 4.7 36.0 1.0
CA I:ASP83 4.7 38.4 1.0
N I:GLY72 4.7 46.8 1.0
N I:HIS80 4.8 45.4 1.0
CA I:HIS80 4.8 43.5 1.0
CA I:HIS63 5.0 42.2 1.0
C I:LYS136 5.0 49.1 1.0
N I:ASP83 5.0 36.3 1.0
C I:HIS71 5.0 47.2 1.0

Zinc binding site 10 out of 10 in 1n18

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Zinc binding site 10 out of 10 in the Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Thermostable Mutant of Human Superoxide Dismutase, C6A, C111S within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn155

b:31.5
occ:1.00
OD1 J:ASP83 1.9 33.8 1.0
ND1 J:HIS71 2.0 34.4 1.0
ND1 J:HIS63 2.0 34.8 1.0
ND1 J:HIS80 2.0 28.0 1.0
CG J:ASP83 2.8 31.3 1.0
CE1 J:HIS71 2.8 33.9 1.0
CE1 J:HIS80 2.9 26.9 1.0
OD2 J:ASP83 2.9 29.6 1.0
CE1 J:HIS63 3.0 32.4 1.0
CG J:HIS80 3.0 30.9 1.0
CG J:HIS63 3.0 31.5 1.0
CG J:HIS71 3.1 33.0 1.0
CB J:HIS63 3.4 33.0 1.0
CB J:HIS80 3.5 31.4 1.0
CB J:HIS71 3.6 32.2 1.0
O J:LYS136 3.8 32.6 1.0
NE2 J:HIS71 4.0 31.9 1.0
NE2 J:HIS80 4.0 27.5 1.0
CA J:HIS71 4.0 33.2 1.0
CD2 J:HIS80 4.1 29.5 1.0
NE2 J:HIS63 4.1 32.1 1.0
CD2 J:HIS71 4.1 32.7 1.0
CD2 J:HIS63 4.2 34.0 1.0
CB J:ASP83 4.2 31.9 1.0
CA J:ASP83 4.7 31.8 1.0
N J:HIS80 4.7 35.6 1.0
CA J:HIS80 4.7 33.5 1.0
C J:LYS136 4.7 32.9 1.0
N J:GLY72 4.7 31.4 1.0
O J:HOH163 4.8 33.0 1.0
N J:ASP83 4.8 31.1 1.0
CD2 J:HIS46 4.9 32.0 1.0
CA J:HIS63 4.9 33.1 1.0
C J:HIS71 5.0 32.4 1.0

Reference:

R.M.F.Cardoso, M.M.Thayer, M.Didonato, T.P.Lo, C.K.Bruns, E.D.Getzoff, J.A.Tainer. Insights Into Lou Gehrig'S Disease From the Structure and Instability of the A4V Mutant of Human Cu,Zn Superoxide Dismutase. J.Mol.Biol. V. 324 247 2002.
ISSN: ISSN 0022-2836
PubMed: 12441104
DOI: 10.1016/S0022-2836(02)01090-2
Page generated: Wed Oct 16 17:09:07 2024

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