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Zinc in PDB 1uxm: A4V Mutant of Human SOD1

Enzymatic activity of A4V Mutant of Human SOD1

All present enzymatic activity of A4V Mutant of Human SOD1:
1.15.1.1;

Protein crystallography data

The structure of A4V Mutant of Human SOD1, PDB code: 1uxm was solved by M.A.Hough, J.G.Grossmann, S.V.Antonyuk, R.W.Strange, P.A.Doucette, J.A.Rodriguez, L.J.Whitson, 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) 27.00 / 1.9
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 112.374, 145.582, 112.497, 90.00, 120.05, 90.00
R / Rfree (%) 22.8 / 25

Other elements in 1uxm:

The structure of A4V Mutant of Human SOD1 also contains other interesting chemical elements:

Copper (Cu) 12 atoms

Zinc Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 12;

Binding sites:

The binding sites of Zinc atom in the A4V Mutant of Human SOD1 (pdb code 1uxm). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 12 binding sites of Zinc where determined in the A4V Mutant of Human SOD1, PDB code: 1uxm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 1uxm

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Zinc binding site 1 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:10.6
occ:1.00
ND1 A:HIS80 1.9 8.9 1.0
OD1 A:ASP83 1.9 7.9 1.0
ND1 A:HIS63 2.0 9.7 1.0
ND1 A:HIS71 2.1 14.0 1.0
CE1 A:HIS80 2.7 10.3 1.0
CG A:ASP83 2.8 6.5 1.0
CE1 A:HIS71 2.9 9.5 1.0
OD2 A:ASP83 3.0 8.8 1.0
CE1 A:HIS63 3.0 10.5 1.0
CG A:HIS63 3.0 8.0 1.0
CG A:HIS80 3.1 10.0 1.0
CG A:HIS71 3.2 10.8 1.0
CB A:HIS63 3.4 8.6 1.0
O A:LYS136 3.6 12.9 1.0
CB A:HIS80 3.7 9.4 1.0
CB A:HIS71 3.7 8.7 1.0
NE2 A:HIS80 3.8 12.6 1.0
CA A:HIS71 4.0 10.1 1.0
CD2 A:HIS80 4.0 11.2 1.0
NE2 A:HIS71 4.1 10.4 1.0
NE2 A:HIS63 4.1 14.9 1.0
CD2 A:HIS63 4.1 10.3 1.0
CB A:ASP83 4.2 10.7 1.0
CD2 A:HIS71 4.3 10.0 1.0
C A:LYS136 4.7 11.3 1.0
CA A:ASP83 4.7 10.0 1.0
N A:HIS80 4.8 9.7 1.0
O A:HOH2061 4.8 24.4 1.0
N A:GLY72 4.8 11.0 1.0
CA A:HIS80 4.9 8.3 1.0
CA A:HIS63 4.9 8.9 1.0
N A:ASP83 4.9 9.3 1.0
N A:HIS71 5.0 9.9 1.0
C A:HIS71 5.0 10.9 1.0

Zinc binding site 2 out of 12 in 1uxm

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Zinc binding site 2 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:12.2
occ:1.00
OD1 B:ASP83 2.0 7.6 1.0
ND1 B:HIS80 2.0 5.5 1.0
ND1 B:HIS71 2.0 13.2 1.0
ND1 B:HIS63 2.0 13.8 1.0
CE1 B:HIS80 2.8 10.7 1.0
CG B:ASP83 2.8 8.0 1.0
CE1 B:HIS71 2.9 10.2 1.0
OD2 B:ASP83 3.0 11.0 1.0
CE1 B:HIS63 3.0 10.6 1.0
CG B:HIS63 3.0 11.8 1.0
CG B:HIS71 3.1 9.4 1.0
CG B:HIS80 3.1 9.9 1.0
CB B:HIS63 3.4 9.6 1.0
CB B:HIS71 3.5 8.5 1.0
O B:LYS136 3.6 13.3 1.0
CB B:HIS80 3.6 9.9 1.0
NE2 B:HIS80 3.9 9.2 1.0
CA B:HIS71 4.0 9.5 1.0
NE2 B:HIS71 4.1 12.2 1.0
CD2 B:HIS80 4.1 8.2 1.0
NE2 B:HIS63 4.1 16.5 1.0
CD2 B:HIS71 4.2 8.9 1.0
CD2 B:HIS63 4.2 11.6 1.0
CB B:ASP83 4.2 9.5 1.0
C B:LYS136 4.6 13.0 1.0
CA B:ASP83 4.7 9.6 1.0
N B:HIS80 4.7 10.5 1.0
CA B:HIS80 4.8 10.4 1.0
N B:GLY72 4.9 9.9 1.0
N B:ASP83 4.9 9.2 1.0
O B:HOH2063 4.9 29.6 1.0
CA B:THR137 4.9 11.2 1.0
CA B:HIS63 4.9 10.5 1.0
N B:HIS71 5.0 9.5 1.0
C B:HIS71 5.0 10.1 1.0

Zinc binding site 3 out of 12 in 1uxm

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Zinc binding site 3 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:11.0
occ:1.00
ND1 C:HIS80 2.0 7.4 1.0
OD1 C:ASP83 2.0 11.2 1.0
ND1 C:HIS63 2.0 10.4 1.0
ND1 C:HIS71 2.0 12.2 1.0
CE1 C:HIS80 2.8 5.7 1.0
CG C:ASP83 2.9 7.8 1.0
CE1 C:HIS71 2.9 9.0 1.0
CE1 C:HIS63 3.0 8.5 1.0
OD2 C:ASP83 3.0 8.2 1.0
CG C:HIS63 3.0 7.7 1.0
CG C:HIS80 3.1 8.2 1.0
CG C:HIS71 3.2 8.5 1.0
CB C:HIS63 3.4 7.8 1.0
CB C:HIS80 3.5 8.1 1.0
CB C:HIS71 3.7 8.4 1.0
O C:LYS136 3.7 12.0 1.0
CA C:HIS71 3.9 9.6 1.0
NE2 C:HIS80 4.0 7.6 1.0
NE2 C:HIS71 4.0 8.6 1.0
CD2 C:HIS80 4.1 7.6 1.0
NE2 C:HIS63 4.1 14.6 1.0
CD2 C:HIS63 4.1 9.7 1.0
CD2 C:HIS71 4.2 8.1 1.0
CB C:ASP83 4.2 9.8 1.0
C C:LYS136 4.7 11.2 1.0
N C:HIS80 4.7 8.2 1.0
CA C:ASP83 4.8 9.4 1.0
CA C:HIS80 4.8 8.9 1.0
N C:GLY72 4.8 10.4 1.0
O C:HOH2064 4.9 26.1 1.0
N C:HIS71 4.9 10.5 1.0
C C:HIS71 4.9 10.3 1.0
CA C:HIS63 4.9 8.6 1.0
N C:ASP83 5.0 8.1 1.0

Zinc binding site 4 out of 12 in 1uxm

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Zinc binding site 4 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:11.1
occ:1.00
OD1 D:ASP83 1.9 10.3 1.0
ND1 D:HIS80 1.9 8.6 1.0
ND1 D:HIS63 2.0 10.4 1.0
ND1 D:HIS71 2.0 12.1 1.0
CG D:ASP83 2.8 12.0 1.0
CE1 D:HIS80 2.8 11.6 1.0
CE1 D:HIS63 2.9 8.6 1.0
CE1 D:HIS71 2.9 12.2 1.0
OD2 D:ASP83 2.9 12.8 1.0
CG D:HIS63 3.0 7.9 1.0
CG D:HIS80 3.1 9.5 1.0
CG D:HIS71 3.1 11.3 1.0
CB D:HIS63 3.4 8.2 1.0
CB D:HIS71 3.5 11.5 1.0
CB D:HIS80 3.6 9.2 1.0
O D:LYS136 3.7 12.7 1.0
NE2 D:HIS80 3.9 10.7 1.0
CA D:HIS71 3.9 11.8 1.0
NE2 D:HIS63 4.0 13.8 1.0
NE2 D:HIS71 4.1 12.9 1.0
CD2 D:HIS80 4.1 7.4 1.0
CD2 D:HIS63 4.1 12.6 1.0
CD2 D:HIS71 4.2 11.4 1.0
CB D:ASP83 4.2 10.2 1.0
C D:LYS136 4.7 12.0 1.0
CA D:ASP83 4.7 9.9 1.0
N D:HIS80 4.8 8.2 1.0
CA D:HIS80 4.8 8.8 1.0
N D:ASP83 4.9 8.9 1.0
O D:HOH2111 4.9 24.4 1.0
N D:GLY72 4.9 11.2 1.0
N D:HIS71 4.9 12.6 1.0
CA D:THR137 4.9 11.5 1.0
C D:HIS71 5.0 12.3 1.0
CA D:HIS63 5.0 7.8 1.0

Zinc binding site 5 out of 12 in 1uxm

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Zinc binding site 5 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn155

b:14.5
occ:1.00
ND1 E:HIS80 1.9 13.7 1.0
OD1 E:ASP83 2.0 11.4 1.0
ND1 E:HIS63 2.0 13.3 1.0
ND1 E:HIS71 2.1 16.7 1.0
CE1 E:HIS80 2.8 12.8 1.0
CG E:ASP83 2.8 11.0 1.0
OD2 E:ASP83 2.9 11.6 1.0
CG E:HIS80 3.0 11.7 1.0
CE1 E:HIS71 3.0 14.4 1.0
CE1 E:HIS63 3.0 11.9 1.0
CG E:HIS63 3.0 13.9 1.0
CG E:HIS71 3.2 15.4 1.0
CB E:HIS63 3.4 12.5 1.0
CB E:HIS80 3.4 13.4 1.0
CB E:HIS71 3.6 15.1 1.0
O E:LYS136 3.7 13.8 1.0
NE2 E:HIS80 3.9 11.6 1.0
CA E:HIS71 3.9 15.0 1.0
CD2 E:HIS80 4.0 11.2 1.0
NE2 E:HIS63 4.1 14.6 1.0
NE2 E:HIS71 4.2 18.6 1.0
CD2 E:HIS63 4.2 14.5 1.0
CB E:ASP83 4.2 11.9 1.0
CD2 E:HIS71 4.3 16.9 1.0
C E:LYS136 4.7 13.8 1.0
CA E:ASP83 4.7 12.2 1.0
CA E:HIS80 4.7 13.5 1.0
N E:HIS80 4.7 14.3 1.0
N E:GLY72 4.8 15.0 1.0
N E:ASP83 4.8 12.8 1.0
C E:HIS71 4.9 15.0 1.0
N E:HIS71 4.9 15.5 1.0
CA E:HIS63 4.9 12.9 1.0

Zinc binding site 6 out of 12 in 1uxm

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Zinc binding site 6 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:13.4
occ:1.00
OD1 F:ASP83 1.9 12.9 1.0
ND1 F:HIS63 1.9 15.1 1.0
ND1 F:HIS71 1.9 16.2 1.0
ND1 F:HIS80 2.1 9.4 1.0
CE1 F:HIS71 2.8 13.8 1.0
CE1 F:HIS80 2.9 12.1 1.0
CE1 F:HIS63 2.9 13.8 1.0
CG F:ASP83 2.9 9.7 1.0
CG F:HIS63 2.9 13.3 1.0
CG F:HIS71 3.1 12.6 1.0
OD2 F:ASP83 3.1 9.8 1.0
CG F:HIS80 3.2 11.5 1.0
CB F:HIS63 3.3 11.4 1.0
CB F:HIS71 3.6 14.4 1.0
O F:LYS136 3.7 17.9 1.0
CB F:HIS80 3.7 12.5 1.0
NE2 F:HIS71 4.0 15.4 1.0
NE2 F:HIS63 4.0 17.9 1.0
CA F:HIS71 4.0 13.8 1.0
CD2 F:HIS63 4.0 13.2 1.0
NE2 F:HIS80 4.0 11.9 1.0
CD2 F:HIS71 4.1 16.4 1.0
CD2 F:HIS80 4.2 14.9 1.0
CB F:ASP83 4.3 11.4 1.0
O F:HOH2020 4.5 32.5 1.0
CA F:ASP83 4.7 11.5 1.0
C F:LYS136 4.8 17.1 1.0
N F:ASP83 4.9 11.4 1.0
CA F:HIS63 4.9 12.7 1.0
N F:GLY72 4.9 13.4 1.0
N F:HIS80 4.9 13.8 1.0
N F:HIS71 5.0 14.0 1.0
CA F:HIS80 5.0 13.4 1.0

Zinc binding site 7 out of 12 in 1uxm

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Zinc binding site 7 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn155

b:12.7
occ:1.00
ND1 G:HIS80 1.9 12.6 1.0
ND1 G:HIS63 1.9 7.5 1.0
OD1 G:ASP83 1.9 14.2 1.0
ND1 G:HIS71 2.0 13.0 1.0
CE1 G:HIS80 2.7 11.6 1.0
CG G:ASP83 2.8 12.5 1.0
CE1 G:HIS63 2.8 6.5 1.0
OD2 G:ASP83 2.9 8.4 1.0
CE1 G:HIS71 2.9 11.8 1.0
CG G:HIS63 3.0 9.1 1.0
CG G:HIS80 3.0 14.7 1.0
CG G:HIS71 3.1 11.1 1.0
CB G:HIS63 3.4 11.2 1.0
CB G:HIS71 3.5 14.8 1.0
CB G:HIS80 3.5 14.7 1.0
O G:LYS136 3.6 12.9 1.0
NE2 G:HIS80 3.9 14.0 1.0
CA G:HIS71 4.0 15.3 1.0
NE2 G:HIS63 4.0 7.9 1.0
CD2 G:HIS80 4.0 12.1 1.0
CD2 G:HIS63 4.1 8.8 1.0
NE2 G:HIS71 4.1 13.7 1.0
CD2 G:HIS71 4.2 10.9 1.0
CB G:ASP83 4.2 13.4 1.0
C G:LYS136 4.6 11.4 1.0
O G:HOH2069 4.7 27.7 1.0
CA G:ASP83 4.7 14.8 1.0
N G:GLY72 4.8 16.0 1.0
N G:HIS80 4.8 18.5 1.0
CA G:HIS80 4.8 17.1 1.0
CA G:THR137 4.9 9.9 1.0
N G:ASP83 4.9 13.4 1.0
C G:HIS71 4.9 15.2 1.0
N G:HIS71 5.0 18.4 1.0
CA G:HIS63 5.0 12.9 1.0

Zinc binding site 8 out of 12 in 1uxm

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Zinc binding site 8 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn155

b:21.2
occ:1.00
ND1 H:HIS80 1.8 16.6 1.0
ND1 H:HIS63 2.0 19.6 1.0
OD1 H:ASP83 2.1 22.1 1.0
ND1 H:HIS71 2.2 10.8 1.0
CE1 H:HIS80 2.8 19.4 1.0
CG H:HIS80 2.9 15.6 1.0
CG H:ASP83 2.9 18.1 1.0
CE1 H:HIS63 2.9 19.8 1.0
CG H:HIS63 3.0 18.5 1.0
CE1 H:HIS71 3.1 15.8 1.0
OD2 H:ASP83 3.1 15.8 1.0
CG H:HIS71 3.2 19.6 1.0
CB H:HIS80 3.3 14.8 1.0
CB H:HIS63 3.4 19.6 1.0
O H:LYS136 3.5 21.4 1.0
CB H:HIS71 3.6 23.1 1.0
O H:HOH2029 3.9 19.2 1.0
NE2 H:HIS80 3.9 19.0 1.0
CD2 H:HIS80 4.0 14.7 1.0
CA H:HIS71 4.0 23.3 1.0
NE2 H:HIS63 4.1 22.4 1.0
CD2 H:HIS63 4.1 19.2 1.0
NE2 H:HIS71 4.2 19.9 1.0
CD2 H:HIS71 4.3 19.6 1.0
CB H:ASP83 4.3 19.1 1.0
C H:LYS136 4.6 20.7 1.0
CA H:HIS80 4.7 13.3 1.0
CA H:ASP83 4.7 19.6 1.0
O H:HOH2028 4.8 41.9 1.0
N H:HIS80 4.8 18.4 1.0
N H:GLY72 4.8 24.2 1.0
N H:ASP83 4.9 18.7 1.0
CA H:HIS63 4.9 19.4 1.0
CD2 H:HIS46 5.0 12.6 1.0

Zinc binding site 9 out of 12 in 1uxm

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Zinc binding site 9 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn155

b:18.3
occ:1.00
ND1 I:HIS80 1.7 16.3 1.0
ND1 I:HIS71 2.1 14.9 1.0
OD1 I:ASP83 2.1 20.2 1.0
ND1 I:HIS63 2.3 13.3 1.0
CE1 I:HIS80 2.5 16.2 1.0
CE1 I:HIS71 2.9 16.2 1.0
CG I:ASP83 2.9 18.9 1.0
CG I:HIS80 2.9 16.8 1.0
OD2 I:ASP83 3.0 19.6 1.0
CG I:HIS71 3.2 15.8 1.0
CG I:HIS63 3.2 15.9 1.0
CE1 I:HIS63 3.3 14.5 1.0
CB I:HIS63 3.4 15.7 1.0
CB I:HIS80 3.5 18.7 1.0
O I:LYS136 3.6 20.3 1.0
CB I:HIS71 3.6 17.4 1.0
NE2 I:HIS80 3.7 16.6 1.0
CD2 I:HIS80 3.9 16.0 1.0
CA I:HIS71 4.0 17.1 1.0
NE2 I:HIS71 4.1 16.1 1.0
CD2 I:HIS71 4.2 16.2 1.0
CB I:ASP83 4.3 18.1 1.0
CD2 I:HIS63 4.4 16.5 1.0
NE2 I:HIS63 4.4 14.6 1.0
C I:LYS136 4.6 20.7 1.0
N I:GLY72 4.7 17.1 1.0
N I:HIS80 4.7 20.6 1.0
CA I:ASP83 4.7 18.8 1.0
CA I:HIS80 4.7 19.3 1.0
CA I:HIS63 4.9 16.5 1.0
N I:ASP83 4.9 18.6 1.0
C I:HIS71 4.9 17.2 1.0
CD2 I:HIS46 4.9 19.0 1.0
N I:HIS71 5.0 18.7 1.0

Zinc binding site 10 out of 12 in 1uxm

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Zinc binding site 10 out of 12 in the A4V Mutant of Human SOD1


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of A4V Mutant of Human SOD1 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn155

b:16.4
occ:1.00
OD1 J:ASP83 1.8 19.3 1.0
ND1 J:HIS80 1.9 17.0 1.0
ND1 J:HIS71 2.0 15.9 1.0
ND1 J:HIS63 2.1 14.0 1.0
CE1 J:HIS80 2.4 14.4 1.0
CG J:ASP83 2.7 17.6 1.0
OD2 J:ASP83 2.8 18.1 1.0
CE1 J:HIS71 2.8 13.5 1.0
CG J:HIS63 3.0 15.3 1.0
CE1 J:HIS63 3.1 16.2 1.0
CG J:HIS71 3.1 15.8 1.0
CG J:HIS80 3.1 14.2 1.0
CB J:HIS63 3.3 13.8 1.0
CB J:HIS71 3.6 16.8 1.0
NE2 J:HIS80 3.6 14.7 1.0
O J:LYS136 3.8 19.4 1.0
CB J:HIS80 3.9 16.4 1.0
CA J:HIS71 3.9 17.0 1.0
CD2 J:HIS80 4.0 15.8 1.0
NE2 J:HIS71 4.0 14.3 1.0
CD2 J:HIS71 4.1 17.9 1.0
CB J:ASP83 4.1 15.0 1.0
NE2 J:HIS63 4.2 15.5 1.0
CD2 J:HIS63 4.2 15.8 1.0
CA J:ASP83 4.7 14.7 1.0
O J:HOH2031 4.8 32.8 1.0
CA J:HIS63 4.9 13.9 1.0
C J:LYS136 4.9 17.6 1.0
N J:GLY72 4.9 16.9 1.0
N J:HIS71 4.9 18.1 1.0
C J:HIS71 4.9 17.2 1.0
N J:HIS80 5.0 16.4 1.0
N J:ASP83 5.0 13.7 1.0

Reference:

M.A.Hough, J.G.Grossmann, S.V.Antonyuk, R.W.Strange, P.A.Doucette, J.A.Rodriguez, L.J.Whitson, P.J.Hart, L.J.Hayward, J.S.Valentine, S.S.Hasnain. Dimer Destabilization in Superoxide Dismutase May Result in Disease-Causing Properties: Structures of Motor Neuron Disease Mutants Proc.Natl.Acad.Sci.Usa V. 101 5976 2004.
ISSN: ISSN 0027-8424
PubMed: 15056757
DOI: 10.1073/PNAS.0305143101
Page generated: Wed Dec 16 03:07:23 2020

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