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Zinc in PDB 1hl5: The Structure of Holo Type Human Cu, Zn Superoxide Dismutase

Enzymatic activity of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase

All present enzymatic activity of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase:
1.15.1.1;

Protein crystallography data

The structure of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase, PDB code: 1hl5 was solved by R.W.Strange, S.Antonyuk, M.A.Hough, P.Doucette, J.Rodriguez, P.J.Hart, L.J.Hayward, J.S.Valentine, S.S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 1.8
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.871, 172.380, 112.450, 90.00, 93.45, 90.00
R / Rfree (%) 18.5 / 22.2

Other elements in 1hl5:

The structure of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase also contains other interesting chemical elements:

Copper (Cu) 18 atoms
Calcium (Ca) 3 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Zinc atom in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase (pdb code 1hl5). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 18 binding sites of Zinc where determined in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase, PDB code: 1hl5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 18 in 1hl5

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Zinc binding site 1 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:8.8
occ:1.00
OD1 A:ASP83 1.9 6.3 1.0
ND1 A:HIS71 2.0 6.5 1.0
ND1 A:HIS80 2.0 7.6 1.0
ND1 A:HIS63 2.0 9.2 1.0
CG A:ASP83 2.7 7.7 1.0
OD2 A:ASP83 2.8 8.9 1.0
CE1 A:HIS71 2.8 7.7 1.0
CE1 A:HIS80 2.9 10.0 1.0
CE1 A:HIS63 3.0 13.6 1.0
CG A:HIS63 3.1 11.5 1.0
CG A:HIS80 3.1 7.5 1.0
CG A:HIS71 3.1 8.8 1.0
CB A:HIS63 3.4 9.7 1.0
CB A:HIS80 3.5 8.6 1.0
CB A:HIS71 3.6 6.9 1.0
O A:LYS136 3.7 9.4 1.0
CA A:HIS71 4.0 9.0 1.0
NE2 A:HIS71 4.0 7.7 1.0
NE2 A:HIS80 4.0 9.8 1.0
NE2 A:HIS63 4.1 17.6 1.0
CD2 A:HIS80 4.1 7.5 1.0
CD2 A:HIS63 4.2 11.9 1.0
CD2 A:HIS71 4.2 8.7 1.0
CB A:ASP83 4.2 8.1 1.0
C A:LYS136 4.7 10.6 1.0
CA A:ASP83 4.7 8.4 1.0
N A:HIS80 4.7 10.3 1.0
O A:HOH2102 4.7 37.9 1.0
CA A:HIS80 4.8 8.6 1.0
N A:GLY72 4.8 9.2 1.0
C A:HIS71 4.9 9.5 1.0
N A:HIS71 4.9 9.2 1.0
CA A:HIS63 5.0 9.0 1.0
N A:ASP83 5.0 7.8 1.0
CA A:THR137 5.0 10.4 1.0

Zinc binding site 2 out of 18 in 1hl5

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Zinc binding site 2 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:5.7
occ:1.00
OD1 B:ASP83 1.9 5.5 1.0
ND1 B:HIS63 2.0 5.5 1.0
ND1 B:HIS80 2.0 5.0 1.0
ND1 B:HIS71 2.0 5.0 1.0
CG B:ASP83 2.8 5.0 1.0
CE1 B:HIS71 2.9 6.4 1.0
CE1 B:HIS80 2.9 6.1 1.0
OD2 B:ASP83 2.9 5.0 1.0
CE1 B:HIS63 2.9 8.5 1.0
CG B:HIS63 3.0 5.8 1.0
CG B:HIS80 3.1 6.0 1.0
CG B:HIS71 3.1 7.3 1.0
CB B:HIS63 3.4 5.0 1.0
CB B:HIS80 3.6 6.0 1.0
CB B:HIS71 3.6 7.0 1.0
O B:LYS136 3.7 8.7 1.0
CA B:HIS71 4.0 8.2 1.0
NE2 B:HIS80 4.0 7.3 1.0
NE2 B:HIS71 4.0 5.6 1.0
NE2 B:HIS63 4.1 13.2 1.0
CD2 B:HIS63 4.1 9.8 1.0
CD2 B:HIS80 4.1 5.0 1.0
CD2 B:HIS71 4.2 5.7 1.0
CB B:ASP83 4.2 5.0 1.0
C B:LYS136 4.7 9.2 1.0
CA B:ASP83 4.7 5.0 1.0
N B:HIS80 4.7 5.2 1.0
O B:HOH2137 4.8 34.4 1.0
N B:GLY72 4.8 6.9 1.0
CA B:HIS80 4.8 5.7 1.0
N B:ASP83 4.9 5.0 1.0
C B:HIS71 4.9 8.8 1.0
CA B:HIS63 4.9 5.0 1.0
N B:HIS71 5.0 8.8 1.0
CA B:THR137 5.0 9.3 1.0

Zinc binding site 3 out of 18 in 1hl5

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Zinc binding site 3 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:5.6
occ:1.00
ND1 C:HIS63 1.9 6.1 1.0
OD1 C:ASP83 2.0 5.0 1.0
ND1 C:HIS71 2.1 7.5 1.0
ND1 C:HIS80 2.1 5.0 1.0
CG C:ASP83 2.8 7.6 1.0
OD2 C:ASP83 2.8 7.7 1.0
CE1 C:HIS63 2.9 8.8 1.0
CE1 C:HIS71 2.9 6.8 1.0
CE1 C:HIS80 3.0 7.3 1.0
CG C:HIS63 3.0 7.4 1.0
CG C:HIS80 3.1 5.8 1.0
CG C:HIS71 3.2 8.3 1.0
CB C:HIS63 3.4 6.2 1.0
CB C:HIS80 3.5 6.4 1.0
CB C:HIS71 3.6 7.4 1.0
O C:LYS136 3.7 8.4 1.0
CA C:HIS71 4.0 7.7 1.0
NE2 C:HIS63 4.0 11.7 1.0
NE2 C:HIS71 4.1 8.1 1.0
CD2 C:HIS63 4.1 9.7 1.0
NE2 C:HIS80 4.1 5.0 1.0
CD2 C:HIS80 4.2 7.7 1.0
CB C:ASP83 4.2 6.0 1.0
CD2 C:HIS71 4.2 7.2 1.0
CA C:ASP83 4.7 5.4 1.0
N C:HIS80 4.7 7.3 1.0
C C:LYS136 4.7 8.6 1.0
N C:GLY72 4.7 7.2 1.0
CA C:HIS80 4.8 6.2 1.0
O C:HOH2128 4.8 37.8 1.0
N C:ASP83 4.9 5.1 1.0
C C:HIS71 4.9 8.5 1.0
CA C:HIS63 4.9 5.9 1.0
N C:HIS71 5.0 7.6 1.0

Zinc binding site 4 out of 18 in 1hl5

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Zinc binding site 4 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:10.1
occ:1.00
OD1 D:ASP83 1.9 9.4 1.0
ND1 D:HIS80 2.0 10.5 1.0
ND1 D:HIS63 2.0 10.7 1.0
ND1 D:HIS71 2.1 11.8 1.0
CG D:ASP83 2.7 12.4 1.0
OD2 D:ASP83 2.8 13.5 1.0
CE1 D:HIS80 2.9 14.2 1.0
CE1 D:HIS71 2.9 10.9 1.0
CE1 D:HIS63 3.0 10.7 1.0
CG D:HIS63 3.0 10.7 1.0
CG D:HIS80 3.1 11.3 1.0
CG D:HIS71 3.2 14.6 1.0
CB D:HIS63 3.4 9.0 1.0
CB D:HIS80 3.5 11.6 1.0
CB D:HIS71 3.6 13.8 1.0
O D:LYS136 3.8 11.9 1.0
CA D:HIS71 4.0 13.7 1.0
NE2 D:HIS80 4.0 14.0 1.0
NE2 D:HIS71 4.1 15.1 1.0
NE2 D:HIS63 4.1 12.6 1.0
CD2 D:HIS80 4.1 10.6 1.0
CD2 D:HIS63 4.1 11.6 1.0
CB D:ASP83 4.2 11.8 1.0
CD2 D:HIS71 4.2 14.0 1.0
N D:HIS80 4.6 12.3 1.0
CA D:ASP83 4.7 11.2 1.0
N D:GLY72 4.7 13.3 1.0
CA D:HIS80 4.7 11.0 1.0
C D:LYS136 4.7 12.7 1.0
CA D:HIS63 4.9 9.6 1.0
O D:HOH2091 4.9 42.1 1.0
N D:ASP83 4.9 10.4 1.0
C D:HIS71 4.9 14.5 1.0
N D:HIS71 4.9 14.5 1.0

Zinc binding site 5 out of 18 in 1hl5

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Zinc binding site 5 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn155

b:8.9
occ:1.00
OD1 E:ASP83 2.0 8.4 1.0
ND1 E:HIS71 2.0 9.9 1.0
ND1 E:HIS80 2.0 7.6 1.0
ND1 E:HIS63 2.0 9.6 1.0
CG E:ASP83 2.7 8.6 1.0
CE1 E:HIS71 2.8 7.0 1.0
OD2 E:ASP83 2.8 10.5 1.0
CE1 E:HIS80 2.9 12.3 1.0
CE1 E:HIS63 3.0 12.7 1.0
CG E:HIS63 3.0 11.4 1.0
CG E:HIS80 3.1 10.4 1.0
CG E:HIS71 3.2 10.1 1.0
CB E:HIS63 3.4 9.3 1.0
CB E:HIS80 3.5 10.4 1.0
CB E:HIS71 3.7 9.8 1.0
O E:LYS136 3.8 11.5 1.0
CA E:HIS71 4.0 10.6 1.0
NE2 E:HIS71 4.0 7.5 1.0
NE2 E:HIS80 4.0 12.5 1.0
NE2 E:HIS63 4.1 15.4 1.0
CD2 E:HIS80 4.1 12.0 1.0
CD2 E:HIS63 4.2 11.7 1.0
CB E:ASP83 4.2 8.6 1.0
CD2 E:HIS71 4.2 10.7 1.0
CA E:ASP83 4.7 8.3 1.0
N E:GLY72 4.7 9.9 1.0
N E:HIS80 4.7 10.5 1.0
C E:LYS136 4.7 11.7 1.0
CA E:HIS80 4.8 10.0 1.0
O E:HOH2099 4.9 35.5 1.0
N E:ASP83 4.9 8.0 1.0
CA E:HIS63 4.9 9.5 1.0
C E:HIS71 4.9 10.5 1.0
N E:HIS71 4.9 11.3 1.0

Zinc binding site 6 out of 18 in 1hl5

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Zinc binding site 6 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:12.3
occ:1.00
OD1 F:ASP83 1.9 11.3 1.0
ND1 F:HIS80 2.0 9.7 1.0
ND1 F:HIS63 2.0 15.4 1.0
ND1 F:HIS71 2.1 12.1 1.0
CG F:ASP83 2.7 14.0 1.0
OD2 F:ASP83 2.8 13.4 1.0
CE1 F:HIS80 2.8 13.1 1.0
CE1 F:HIS71 2.9 12.3 1.0
CE1 F:HIS63 3.0 17.5 1.0
CG F:HIS80 3.0 13.9 1.0
CG F:HIS63 3.0 14.6 1.0
CG F:HIS71 3.2 11.0 1.0
CB F:HIS63 3.4 12.6 1.0
CB F:HIS80 3.5 13.9 1.0
CB F:HIS71 3.6 12.5 1.0
O F:LYS136 3.7 15.7 1.0
CA F:HIS71 3.9 12.6 1.0
NE2 F:HIS80 3.9 13.1 1.0
CD2 F:HIS80 4.0 13.2 1.0
NE2 F:HIS71 4.1 14.9 1.0
NE2 F:HIS63 4.1 17.4 1.0
CD2 F:HIS63 4.1 14.5 1.0
CB F:ASP83 4.2 12.7 1.0
CD2 F:HIS71 4.2 13.6 1.0
C F:LYS136 4.7 16.2 1.0
N F:HIS80 4.7 13.6 1.0
CA F:ASP83 4.7 13.4 1.0
CA F:HIS80 4.7 13.7 1.0
N F:GLY72 4.8 13.4 1.0
C F:HIS71 4.9 13.3 1.0
N F:ASP83 4.9 12.6 1.0
O F:HOH2078 4.9 37.1 1.0
CA F:HIS63 5.0 11.7 1.0
N F:HIS71 5.0 12.8 1.0
CA F:THR137 5.0 16.3 1.0

Zinc binding site 7 out of 18 in 1hl5

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Zinc binding site 7 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn155

b:20.9
occ:1.00
OD1 G:ASP83 1.9 15.4 1.0
ND1 G:HIS80 1.9 20.5 1.0
ND1 G:HIS63 2.1 21.2 1.0
ND1 G:HIS71 2.1 22.2 1.0
CG G:ASP83 2.6 19.5 1.0
OD2 G:ASP83 2.7 18.5 1.0
CE1 G:HIS80 2.9 22.1 1.0
CG G:HIS80 3.0 20.7 1.0
CE1 G:HIS71 3.0 21.2 1.0
CE1 G:HIS63 3.1 20.9 1.0
CG G:HIS63 3.1 21.0 1.0
CG G:HIS71 3.2 22.9 1.0
CB G:HIS80 3.4 20.9 1.0
CB G:HIS63 3.4 20.2 1.0
CB G:HIS71 3.5 22.5 1.0
O G:LYS136 3.6 27.6 1.0
CA G:HIS71 3.9 22.6 1.0
NE2 G:HIS80 4.0 21.8 1.0
CB G:ASP83 4.1 19.4 1.0
CD2 G:HIS80 4.1 19.5 1.0
NE2 G:HIS71 4.2 22.5 1.0
NE2 G:HIS63 4.2 20.2 1.0
CD2 G:HIS63 4.2 20.9 1.0
CD2 G:HIS71 4.3 21.8 1.0
CA G:ASP83 4.6 18.6 1.0
C G:LYS136 4.6 27.6 1.0
N G:HIS80 4.6 21.0 1.0
CA G:HIS80 4.6 21.0 1.0
N G:GLY72 4.7 21.8 1.0
N G:ASP83 4.8 19.1 1.0
C G:HIS71 4.9 22.1 1.0
CA G:HIS63 5.0 20.2 1.0
N G:HIS71 5.0 22.9 1.0

Zinc binding site 8 out of 18 in 1hl5

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Zinc binding site 8 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn155

b:10.2
occ:1.00
ND1 H:HIS80 1.9 12.1 1.0
OD1 H:ASP83 2.0 9.6 1.0
ND1 H:HIS63 2.0 9.3 1.0
ND1 H:HIS71 2.1 8.3 1.0
CE1 H:HIS80 2.7 15.9 1.0
CG H:ASP83 2.8 9.7 1.0
OD2 H:ASP83 2.9 9.6 1.0
CE1 H:HIS71 2.9 9.1 1.0
CE1 H:HIS63 3.0 11.6 1.0
CG H:HIS80 3.0 13.1 1.0
CG H:HIS63 3.1 11.5 1.0
CG H:HIS71 3.2 12.5 1.0
CB H:HIS63 3.5 8.5 1.0
CB H:HIS80 3.5 11.1 1.0
CB H:HIS71 3.6 11.6 1.0
O H:LYS136 3.8 13.5 1.0
NE2 H:HIS80 3.9 12.5 1.0
CA H:HIS71 3.9 12.7 1.0
CD2 H:HIS80 4.0 14.3 1.0
NE2 H:HIS71 4.1 11.1 1.0
NE2 H:HIS63 4.1 12.5 1.0
CD2 H:HIS63 4.2 11.4 1.0
CD2 H:HIS71 4.2 12.0 1.0
CB H:ASP83 4.2 9.2 1.0
N H:HIS80 4.7 11.3 1.0
O H:HOH2108 4.7 44.0 1.0
CA H:ASP83 4.7 9.2 1.0
CA H:HIS80 4.7 10.9 1.0
C H:LYS136 4.8 13.8 1.0
N H:GLY72 4.8 11.4 1.0
C H:HIS71 4.9 12.5 1.0
N H:HIS71 4.9 13.6 1.0
N H:ASP83 4.9 8.0 1.0
CA H:HIS63 5.0 9.9 1.0

Zinc binding site 9 out of 18 in 1hl5

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Zinc binding site 9 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn155

b:7.3
occ:1.00
ND1 I:HIS63 1.9 5.5 1.0
OD1 I:ASP83 2.0 6.4 1.0
ND1 I:HIS71 2.1 6.7 1.0
ND1 I:HIS80 2.1 6.7 1.0
CG I:ASP83 2.8 8.3 1.0
OD2 I:ASP83 2.8 7.2 1.0
CE1 I:HIS63 2.9 7.3 1.0
CE1 I:HIS71 2.9 6.8 1.0
CE1 I:HIS80 3.0 10.0 1.0
CG I:HIS63 3.0 7.5 1.0
CG I:HIS80 3.1 6.9 1.0
CG I:HIS71 3.1 8.6 1.0
CB I:HIS63 3.4 5.2 1.0
CB I:HIS80 3.5 6.7 1.0
CB I:HIS71 3.5 8.7 1.0
O I:LYS136 3.8 9.9 1.0
CA I:HIS71 3.9 8.2 1.0
NE2 I:HIS63 4.0 11.3 1.0
NE2 I:HIS80 4.1 8.4 1.0
CD2 I:HIS63 4.1 7.5 1.0
NE2 I:HIS71 4.1 6.2 1.0
CD2 I:HIS80 4.2 7.8 1.0
CD2 I:HIS71 4.2 7.0 1.0
CB I:ASP83 4.2 5.0 1.0
N I:HIS80 4.7 8.4 1.0
CA I:ASP83 4.7 6.7 1.0
CA I:HIS80 4.8 7.8 1.0
N I:GLY72 4.8 8.1 1.0
O I:HOH2123 4.8 35.1 1.0
C I:LYS136 4.8 10.0 1.0
N I:ASP83 4.9 5.0 1.0
C I:HIS71 4.9 8.5 1.0
N I:HIS71 4.9 8.8 1.0
CA I:HIS63 5.0 6.5 1.0

Zinc binding site 10 out of 18 in 1hl5

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Zinc binding site 10 out of 18 in the The Structure of Holo Type Human Cu, Zn Superoxide Dismutase


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of The Structure of Holo Type Human Cu, Zn Superoxide Dismutase within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn155

b:6.9
occ:1.00
ND1 J:HIS63 2.0 7.8 1.0
ND1 J:HIS80 2.0 7.5 1.0
OD1 J:ASP83 2.0 5.0 1.0
ND1 J:HIS71 2.1 7.5 1.0
CG J:ASP83 2.8 5.0 1.0
CE1 J:HIS71 2.8 8.0 1.0
CE1 J:HIS80 2.9 8.2 1.0
CE1 J:HIS63 2.9 8.0 1.0
OD2 J:ASP83 2.9 5.6 1.0
CG J:HIS63 3.0 6.8 1.0
CG J:HIS80 3.1 5.0 1.0
CG J:HIS71 3.2 10.6 1.0
CB J:HIS63 3.4 5.8 1.0
CB J:HIS80 3.6 6.5 1.0
CB J:HIS71 3.7 8.7 1.0
O J:LYS136 3.7 10.8 1.0
CA J:HIS71 4.0 8.4 1.0
NE2 J:HIS63 4.0 13.7 1.0
NE2 J:HIS80 4.0 7.5 1.0
NE2 J:HIS71 4.0 8.0 1.0
CD2 J:HIS63 4.1 10.7 1.0
CD2 J:HIS80 4.1 6.7 1.0
CD2 J:HIS71 4.2 8.1 1.0
CB J:ASP83 4.3 5.2 1.0
CA J:ASP83 4.7 5.0 1.0
C J:LYS136 4.7 11.0 1.0
N J:HIS80 4.7 6.5 1.0
N J:GLY72 4.8 6.8 1.0
CA J:HIS80 4.8 6.3 1.0
O J:HOH2120 4.8 32.7 1.0
N J:ASP83 4.9 5.0 1.0
C J:HIS71 4.9 8.6 1.0
N J:HIS71 4.9 9.0 1.0
CA J:HIS63 5.0 5.0 1.0

Reference:

R.W.Strange, S.Antonyuk, M.A.Hough, P.Doucette, J.Rodriguez, P.J.Hart, L.J.Hayward, J.S.Valentine, S.S.Hasnain. The Structure of Holo and Metal-Deficient Wild-Type Human Cu, Zn Superoxide Dismutase and Its Relevance to Familial Amyotrophic Lateral Sclerosis J.Mol.Biol. V. 328 877 2003.
ISSN: ISSN 0022-2836
PubMed: 12729761
DOI: 10.1016/S0022-2836(03)00355-3
Page generated: Wed Dec 16 02:51:18 2020

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