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Zinc in PDB 4b3e: Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.

Enzymatic activity of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.

All present enzymatic activity of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.:
1.15.1.1;

Protein crystallography data

The structure of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate., PDB code: 4b3e was solved by R.W.Strange, M.A.Hough, S.V.Antonyuk, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.15
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 165.994, 203.107, 144.384, 90.00, 90.00, 90.00
R / Rfree (%) 17.467 / 21.496

Other elements in 4b3e:

The structure of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. also contains other interesting chemical elements:

Copper (Cu) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. (pdb code 4b3e). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate., PDB code: 4b3e:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 4b3e

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Zinc binding site 1 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:22.6
occ:1.00
 OD1 A:ASP83 1.9 17.5 1.0
ND1 A:HIS63 1.9 21.7 1.0
ND1 A:HIS80 2.0 22.6 1.0
ND1 A:HIS71 2.1 25.1 1.0
CG A:ASP83 2.7 18.1 1.0
CE1 A:HIS80 2.8 22.9 1.0
CE1 A:HIS63 2.9 22.5 1.0
OD2 A:ASP83 2.9 18.1 1.0
CE1 A:HIS71 2.9 24.8 1.0
CG A:HIS63 3.0 21.2 1.0
CG A:HIS80 3.1 22.4 1.0
CG A:HIS71 3.2 25.6 1.0
CB A:HIS63 3.4 20.3 1.0
CB A:HIS80 3.6 21.7 1.0
CB A:HIS71 3.6 26.0 1.0
CA A:HIS71 4.0 26.6 1.0
NE2 A:HIS80 4.0 22.8 1.0
NE2 A:HIS63 4.0 22.6 1.0
O A:LYS136 4.0 36.4 1.0
CD2 A:HIS63 4.1 21.6 1.0
NE2 A:HIS71 4.1 25.7 1.0
CB A:ASP83 4.2 18.1 1.0
CD2 A:HIS80 4.2 23.2 1.0
CD2 A:HIS71 4.2 25.8 1.0
CA A:ASP83 4.7 18.0 1.0
N A:HIS80 4.7 23.1 1.0
N A:GLY72 4.8 25.9 1.0
CA A:HIS80 4.8 22.1 1.0
N A:ASP83 4.8 18.0 1.0
C A:HIS71 4.9 26.1 1.0
CA A:HIS63 4.9 19.7 1.0
O A:GLY72 5.0 24.3 1.0
N A:HIS71 5.0 27.7 1.0
O A:HOH2098 5.0 29.0 1.0

Zinc binding site 2 out of 10 in 4b3e

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Zinc binding site 2 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:30.0
occ:0.75
 ND1 B:HIS80 1.6 34.0 1.0
OD1 B:ASP83 1.9 31.3 1.0
ND1 B:HIS71 2.1 40.5 1.0
ND1 B:HIS63 2.1 39.9 1.0
CE1 B:HIS80 2.3 34.0 1.0
CG B:ASP83 2.6 33.6 1.0
OD2 B:ASP83 2.8 34.0 1.0
CG B:HIS80 2.8 35.2 1.0
CE1 B:HIS71 2.9 39.9 1.0
CE1 B:HIS63 3.0 40.7 1.0
CG B:HIS63 3.1 37.8 1.0
CG B:HIS71 3.2 41.5 1.0
CB B:HIS63 3.5 35.3 1.0
NE2 B:HIS80 3.5 35.9 1.0
CB B:HIS80 3.5 34.6 1.0
CB B:HIS71 3.6 42.8 1.0
CD2 B:HIS80 3.8 35.0 1.0
CA B:HIS71 4.0 44.1 1.0
CB B:ASP83 4.1 33.4 1.0
NE2 B:HIS63 4.1 41.2 1.0
NE2 B:HIS71 4.1 40.7 1.0
CD2 B:HIS63 4.1 39.1 1.0
O B:LYS136 4.1 51.8 1.0
CD2 B:HIS71 4.2 41.3 1.0
CA B:ASP83 4.6 32.2 1.0
N B:HIS80 4.6 38.6 1.0
CA B:HIS80 4.7 35.7 1.0
N B:GLY72 4.8 44.0 1.0
N B:ASP83 4.8 32.1 1.0
C B:HIS71 4.9 44.9 1.0
O B:GLY72 5.0 42.3 1.0

Zinc binding site 3 out of 10 in 4b3e

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Zinc binding site 3 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:17.8
occ:1.00
 OD1 C:ASP83 1.9 16.9 1.0
ND1 C:HIS71 2.0 20.8 1.0
ND1 C:HIS80 2.0 19.9 1.0
ND1 C:HIS63 2.1 17.8 1.0
CG C:ASP83 2.7 17.3 1.0
OD2 C:ASP83 2.9 17.6 1.0
CE1 C:HIS80 2.9 20.4 1.0
CE1 C:HIS71 2.9 20.4 1.0
CE1 C:HIS63 3.0 18.2 1.0
CG C:HIS63 3.1 18.0 1.0
CG C:HIS80 3.1 19.9 1.0
CG C:HIS71 3.1 21.0 1.0
CB C:HIS63 3.4 17.9 1.0
CB C:HIS71 3.5 21.4 1.0
CB C:HIS80 3.6 19.4 1.0
O C:LYS136 3.7 25.1 1.0
CA C:HIS71 3.9 22.3 1.0
NE2 C:HIS80 4.0 20.9 1.0
NE2 C:HIS71 4.1 20.3 1.0
CD2 C:HIS80 4.2 20.8 1.0
CB C:ASP83 4.2 16.9 1.0
NE2 C:HIS63 4.2 18.4 1.0
CD2 C:HIS71 4.2 20.4 1.0
CD2 C:HIS63 4.2 18.0 1.0
O C:HOH2114 4.6 18.0 1.0
N C:HIS80 4.7 19.9 1.0
C C:LYS136 4.7 26.8 1.0
CA C:ASP83 4.7 16.7 1.0
CA C:HIS80 4.7 19.3 1.0
N C:GLY72 4.8 21.4 1.0
C C:HIS71 4.9 22.2 1.0
N C:HIS71 4.9 23.6 1.0
N C:ASP83 4.9 16.8 1.0
CA C:HIS63 4.9 17.9 1.0

Zinc binding site 4 out of 10 in 4b3e

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Zinc binding site 4 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:40.0
occ:1.00
 OD1 D:ASP83 1.9 32.5 1.0
ND1 D:HIS80 2.1 39.8 1.0
ND1 D:HIS63 2.1 33.0 1.0
ND1 D:HIS71 2.2 43.9 1.0
CG D:ASP83 2.8 35.5 1.0
CE1 D:HIS80 2.9 41.2 1.0
CE1 D:HIS71 3.0 42.9 1.0
OD2 D:ASP83 3.0 36.5 1.0
CE1 D:HIS63 3.0 33.2 1.0
CG D:HIS63 3.1 32.5 1.0
CG D:HIS80 3.1 40.7 1.0
CG D:HIS71 3.2 46.2 1.0
CB D:HIS63 3.4 32.2 1.0
CB D:HIS80 3.6 40.4 1.0
CB D:HIS71 3.7 48.0 1.0
O D:LYS136 4.0 59.6 1.0
CA D:HIS71 4.0 49.9 1.0
NE2 D:HIS80 4.1 41.9 1.0
CD2 D:HIS80 4.2 41.7 1.0
NE2 D:HIS63 4.2 33.4 1.0
CB D:ASP83 4.2 35.2 1.0
NE2 D:HIS71 4.2 44.3 1.0
CD2 D:HIS63 4.2 32.2 1.0
CD2 D:HIS71 4.3 46.0 1.0
CA D:ASP83 4.7 33.7 1.0
N D:HIS80 4.7 43.4 1.0
CA D:HIS80 4.8 41.0 1.0
N D:GLY72 4.8 50.5 1.0
N D:ASP83 4.9 35.0 1.0
C D:HIS71 4.9 51.0 1.0
CA D:HIS63 4.9 31.3 1.0

Zinc binding site 5 out of 10 in 4b3e

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Zinc binding site 5 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn155

b:35.5
occ:1.00
 OD1 E:ASP83 1.9 33.0 1.0
ND1 E:HIS63 2.1 40.9 1.0
ND1 E:HIS80 2.1 39.1 1.0
ND1 E:HIS71 2.1 38.0 1.0
CG E:ASP83 2.7 32.8 1.0
OD2 E:ASP83 2.8 32.6 1.0
CE1 E:HIS80 2.9 39.8 1.0
CE1 E:HIS71 2.9 37.4 1.0
CE1 E:HIS63 3.0 40.8 1.0
CG E:HIS63 3.1 40.9 1.0
CG E:HIS80 3.1 39.4 1.0
CG E:HIS71 3.2 40.2 1.0
CB E:HIS63 3.4 40.6 1.0
CB E:HIS80 3.7 37.7 1.0
CB E:HIS71 3.7 41.7 1.0
O E:LYS136 3.9 51.8 1.0
CA E:HIS71 4.0 42.6 1.0
NE2 E:HIS80 4.0 41.4 1.0
NE2 E:HIS71 4.1 38.0 1.0
CB E:ASP83 4.2 31.7 1.0
NE2 E:HIS63 4.2 41.0 1.0
CD2 E:HIS80 4.2 40.9 1.0
CD2 E:HIS63 4.2 40.4 1.0
CD2 E:HIS71 4.3 39.1 1.0
CA E:ASP83 4.7 30.4 1.0
N E:HIS80 4.7 38.2 1.0
CA E:HIS80 4.8 37.5 1.0
C E:LYS136 4.8 55.5 1.0
N E:GLY72 4.9 40.0 1.0
O E:HOH2057 4.9 43.3 1.0
N E:ASP83 4.9 30.6 1.0
N E:HIS71 5.0 44.4 1.0
CA E:HIS63 5.0 39.8 1.0
C E:HIS71 5.0 41.7 1.0

Zinc binding site 6 out of 10 in 4b3e

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Zinc binding site 6 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:13.4
occ:1.00
 ND1 F:HIS63 1.9 14.9 1.0
OD1 F:ASP83 1.9 12.4 1.0
ND1 F:HIS71 2.0 16.0 1.0
ND1 F:HIS80 2.1 14.5 1.0
CG F:ASP83 2.7 12.6 1.0
CE1 F:HIS63 2.8 14.9 1.0
OD2 F:ASP83 2.8 12.9 1.0
CE1 F:HIS71 2.9 15.9 1.0
CE1 F:HIS80 2.9 14.7 1.0
CG F:HIS63 3.0 15.0 1.0
CG F:HIS80 3.1 14.6 1.0
CG F:HIS71 3.2 16.6 1.0
CB F:HIS63 3.4 15.0 1.0
CB F:HIS80 3.6 14.3 1.0
CB F:HIS71 3.7 17.1 1.0
O F:LYS136 3.8 20.0 1.0
NE2 F:HIS63 4.0 14.9 1.0
CA F:HIS71 4.0 17.6 1.0
NE2 F:HIS80 4.1 15.0 1.0
CD2 F:HIS63 4.1 15.0 1.0
NE2 F:HIS71 4.1 15.9 1.0
CB F:ASP83 4.1 12.4 1.0
CD2 F:HIS80 4.2 14.9 1.0
CD2 F:HIS71 4.2 16.3 1.0
O F:HOH2120 4.7 19.6 1.0
CA F:ASP83 4.7 12.2 1.0
N F:HIS80 4.8 14.8 1.0
C F:LYS136 4.8 20.1 1.0
CA F:HIS80 4.8 14.4 1.0
N F:GLY72 4.8 16.4 1.0
N F:ASP83 4.9 12.3 1.0
CA F:HIS63 4.9 15.1 1.0
C F:HIS71 4.9 17.3 1.0
N F:HIS71 5.0 18.6 1.0

Zinc binding site 7 out of 10 in 4b3e

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Zinc binding site 7 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn155

b:13.7
occ:1.00
 OD1 G:ASP83 1.9 13.2 1.0
ND1 G:HIS63 2.0 15.5 1.0
ND1 G:HIS80 2.0 15.2 1.0
ND1 G:HIS71 2.1 15.5 1.0
CG G:ASP83 2.7 13.4 1.0
CE1 G:HIS71 2.9 15.2 1.0
CE1 G:HIS80 2.9 15.5 1.0
OD2 G:ASP83 2.9 13.6 1.0
CE1 G:HIS63 3.0 15.3 1.0
CG G:HIS63 3.0 15.6 1.0
CG G:HIS80 3.1 15.2 1.0
CG G:HIS71 3.2 15.8 1.0
CB G:HIS63 3.4 15.8 1.0
CB G:HIS80 3.6 14.9 1.0
CB G:HIS71 3.7 16.5 1.0
O G:LYS136 3.8 17.0 1.0
CA G:HIS71 4.0 17.0 1.0
NE2 G:HIS80 4.1 15.8 1.0
NE2 G:HIS71 4.1 15.2 1.0
NE2 G:HIS63 4.1 15.5 1.0
CB G:ASP83 4.1 13.3 1.0
CD2 G:HIS63 4.2 15.8 1.0
CD2 G:HIS80 4.2 15.6 1.0
CD2 G:HIS71 4.3 15.5 1.0
CA G:ASP83 4.7 13.1 1.0
C G:LYS136 4.8 17.3 1.0
N G:GLY72 4.8 16.0 1.0
CA G:HIS80 4.8 15.1 1.0
N G:HIS80 4.8 15.2 1.0
O G:HOH2101 4.8 14.3 1.0
N G:ASP83 4.9 13.2 1.0
CA G:HIS63 4.9 16.1 1.0
C G:HIS71 5.0 16.7 1.0
N G:HIS71 5.0 18.7 1.0

Zinc binding site 8 out of 10 in 4b3e

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Zinc binding site 8 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn155

b:14.1
occ:1.00
 OD1 H:ASP83 1.9 13.1 1.0
ND1 H:HIS63 1.9 14.2 1.0
ND1 H:HIS80 2.1 14.7 1.0
ND1 H:HIS71 2.1 15.5 1.0
CG H:ASP83 2.7 13.3 1.0
CE1 H:HIS63 2.8 14.1 1.0
OD2 H:ASP83 2.9 13.6 1.0
CE1 H:HIS80 2.9 14.9 1.0
CE1 H:HIS71 3.0 15.2 1.0
CG H:HIS63 3.0 14.2 1.0
CG H:HIS80 3.2 15.0 1.0
CG H:HIS71 3.2 15.9 1.0
CB H:HIS63 3.5 14.2 1.0
CB H:HIS71 3.6 16.4 1.0
CB H:HIS80 3.6 14.9 1.0
O H:LYS136 3.7 17.4 1.0
CA H:HIS71 4.0 17.0 1.0
NE2 H:HIS63 4.0 14.1 1.0
CD2 H:HIS63 4.1 14.1 1.0
NE2 H:HIS80 4.1 15.2 1.0
NE2 H:HIS71 4.1 15.1 1.0
CB H:ASP83 4.2 13.2 1.0
CD2 H:HIS80 4.2 15.3 1.0
CD2 H:HIS71 4.3 15.4 1.0
C H:LYS136 4.7 18.0 1.0
N H:HIS80 4.7 15.7 1.0
CA H:ASP83 4.7 13.1 1.0
N H:GLY72 4.8 16.6 1.0
CA H:HIS80 4.8 15.1 1.0
O H:HOH2088 4.9 15.7 1.0
N H:HIS71 4.9 17.9 1.0
C H:HIS71 4.9 17.0 1.0
CA H:HIS63 5.0 14.3 1.0
N H:ASP83 5.0 13.1 1.0

Zinc binding site 9 out of 10 in 4b3e

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Zinc binding site 9 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn155

b:19.3
occ:1.00
 OD1 I:ASP83 1.9 17.1 1.0
ND1 I:HIS63 1.9 20.9 1.0
ND1 I:HIS71 2.0 19.2 1.0
ND1 I:HIS80 2.0 20.5 1.0
CG I:ASP83 2.7 18.0 1.0
CE1 I:HIS63 2.8 20.7 1.0
CE1 I:HIS80 2.8 21.1 1.0
OD2 I:ASP83 2.8 18.3 1.0
CE1 I:HIS71 2.8 19.1 1.0
CG I:HIS63 3.0 21.3 1.0
CG I:HIS80 3.1 21.1 1.0
CG I:HIS71 3.1 20.2 1.0
CB I:HIS63 3.5 21.7 1.0
CB I:HIS80 3.6 21.0 1.0
CB I:HIS71 3.6 21.2 1.0
O I:LYS136 3.7 24.6 1.0
CA I:HIS71 3.9 22.1 1.0
NE2 I:HIS63 4.0 20.8 1.0
NE2 I:HIS80 4.0 21.6 1.0
NE2 I:HIS71 4.0 19.1 1.0
CD2 I:HIS63 4.1 21.4 1.0
CD2 I:HIS80 4.1 21.3 1.0
CB I:ASP83 4.1 17.9 1.0
CD2 I:HIS71 4.2 19.5 1.0
C I:LYS136 4.7 25.8 1.0
CA I:ASP83 4.7 17.7 1.0
N I:HIS80 4.7 21.4 1.0
CA I:HIS80 4.8 20.9 1.0
N I:GLY72 4.8 21.0 1.0
O I:HOH2091 4.8 28.8 1.0
C I:HIS71 4.9 22.1 1.0
N I:HIS71 4.9 23.2 1.0
N I:ASP83 4.9 17.9 1.0
CA I:HIS63 4.9 22.0 1.0

Zinc binding site 10 out of 10 in 4b3e

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Zinc binding site 10 out of 10 in the Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate.


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Structure of Copper-Zinc Superoxide Dismutase Complexed with Bicarbonate. within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn155

b:20.2
occ:1.00
 OD1 J:ASP83 1.9 20.2 1.0
ND1 J:HIS63 2.0 23.1 1.0
ND1 J:HIS80 2.0 20.6 1.0
ND1 J:HIS71 2.1 21.9 1.0
CG J:ASP83 2.7 20.6 1.0
OD2 J:ASP83 2.8 20.6 1.0
CE1 J:HIS63 2.9 23.3 1.0
CE1 J:HIS80 3.0 21.0 1.0
CG J:HIS63 3.0 23.6 1.0
CE1 J:HIS71 3.0 21.7 1.0
CG J:HIS80 3.1 21.6 1.0
CG J:HIS71 3.2 22.5 1.0
CB J:HIS63 3.4 23.4 1.0
CB J:HIS80 3.5 22.0 1.0
CB J:HIS71 3.6 23.5 1.0
O J:LYS136 3.9 23.6 1.0
CA J:HIS71 3.9 24.0 1.0
NE2 J:HIS63 4.1 23.6 1.0
NE2 J:HIS80 4.1 21.9 1.0
CD2 J:HIS63 4.1 23.6 1.0
CB J:ASP83 4.2 20.2 1.0
CD2 J:HIS80 4.2 22.2 1.0
NE2 J:HIS71 4.2 21.7 1.0
CD2 J:HIS71 4.3 21.9 1.0
CA J:ASP83 4.6 20.2 1.0
N J:HIS80 4.7 23.4 1.0
CA J:HIS80 4.7 22.8 1.0
N J:GLY72 4.8 23.3 1.0
C J:LYS136 4.8 24.1 1.0
O J:HOH2058 4.8 26.5 1.0
N J:ASP83 4.8 20.5 1.0
C J:HIS71 4.9 23.6 1.0
N J:HIS71 4.9 25.8 1.0
CA J:HIS63 4.9 23.5 1.0

Reference:

R.W.Strange, M.A.Hough, S.V.Antonyuk, S.S.Hasnain. Structural Evidence For A Copper-Bound Carbonate Intermediate in the Peroxidase and Dismutase Activities of Superoxide Dismutase. Plos One V. 7 44811 2012.
ISSN: ISSN 1932-6203
PubMed: 22984565
DOI: 10.1371/JOURNAL.PONE.0044811
Page generated: Sat Oct 26 19:31:20 2024

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