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Zinc in PDB 3gzo: Human SOD1 G93A Variant

Enzymatic activity of Human SOD1 G93A Variant

All present enzymatic activity of Human SOD1 G93A Variant:
1.15.1.1;

Protein crystallography data

The structure of Human SOD1 G93A Variant, PDB code: 3gzo was solved by A.Galaleldeen, A.B.Taylor, N.Narayana, L.J.Whitson, P.J.Hart, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 41.49 / 2.10
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 166.148, 203.263, 143.319, 90.00, 90.00, 90.00
R / Rfree (%) 17.2 / 21.4

Other elements in 3gzo:

The structure of Human SOD1 G93A Variant also contains other interesting chemical elements:

Copper (Cu) 10 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Human SOD1 G93A Variant (pdb code 3gzo). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 10 binding sites of Zinc where determined in the Human SOD1 G93A Variant, PDB code: 3gzo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 10 in 3gzo

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Zinc binding site 1 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn155

b:20.0
occ:1.00
OD1 A:ASP83 1.9 16.1 1.0
ND1 A:HIS80 2.1 17.4 1.0
ND1 A:HIS71 2.1 19.5 1.0
ND1 A:HIS63 2.1 16.7 1.0
CG A:ASP83 2.7 18.9 1.0
OD2 A:ASP83 2.9 19.0 1.0
CE1 A:HIS80 3.0 18.2 1.0
CE1 A:HIS71 3.0 17.0 1.0
CG A:HIS63 3.1 19.2 1.0
CG A:HIS80 3.1 18.4 1.0
CE1 A:HIS63 3.1 19.3 1.0
CG A:HIS71 3.2 18.6 1.0
CB A:HIS63 3.4 17.5 1.0
CB A:HIS80 3.5 17.0 1.0
CB A:HIS71 3.5 17.2 1.0
O A:LYS136 3.9 22.6 1.0
CA A:HIS71 3.9 17.8 1.0
NE2 A:HIS80 4.1 18.7 1.0
CB A:ASP83 4.1 16.3 1.0
CD2 A:HIS80 4.2 18.2 1.0
NE2 A:HIS71 4.2 19.7 1.0
NE2 A:HIS63 4.2 20.7 1.0
CD2 A:HIS63 4.2 17.3 1.0
CD2 A:HIS71 4.3 19.3 1.0
CA A:ASP83 4.6 16.9 1.0
CA A:HIS80 4.8 16.6 1.0
N A:GLY72 4.8 20.4 1.0
N A:HIS80 4.8 17.8 1.0
C A:HIS71 4.9 22.4 1.0
N A:ASP83 4.9 15.5 1.0
CA A:HIS63 4.9 15.9 1.0
C A:LYS136 4.9 25.1 1.0
N A:HIS71 4.9 21.7 1.0
CD2 A:HIS46 5.0 18.6 1.0
O A:HOH299 5.0 20.0 1.0

Zinc binding site 2 out of 10 in 3gzo

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Zinc binding site 2 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn155

b:17.1
occ:1.00
OD1 B:ASP83 1.9 12.8 1.0
ND1 B:HIS71 2.1 13.0 1.0
ND1 B:HIS63 2.1 16.4 1.0
ND1 B:HIS80 2.1 14.7 1.0
CG B:ASP83 2.7 15.5 1.0
OD2 B:ASP83 2.9 14.3 1.0
CE1 B:HIS71 2.9 15.2 1.0
CE1 B:HIS80 3.0 15.7 1.0
CG B:HIS63 3.0 16.5 1.0
CE1 B:HIS63 3.0 14.9 1.0
CG B:HIS71 3.1 16.2 1.0
CG B:HIS80 3.1 15.2 1.0
CB B:HIS63 3.3 13.6 1.0
CB B:HIS80 3.5 15.2 1.0
CB B:HIS71 3.6 14.9 1.0
O B:LYS136 3.9 18.2 1.0
CA B:HIS71 3.9 16.6 1.0
NE2 B:HIS71 4.1 16.4 1.0
NE2 B:HIS80 4.1 16.4 1.0
NE2 B:HIS63 4.2 19.4 1.0
CB B:ASP83 4.2 14.5 1.0
CD2 B:HIS63 4.2 15.5 1.0
CD2 B:HIS71 4.2 17.4 1.0
CD2 B:HIS80 4.2 18.2 1.0
CA B:ASP83 4.7 14.6 1.0
N B:HIS80 4.7 14.5 1.0
CA B:HIS80 4.7 14.9 1.0
N B:GLY72 4.8 14.9 1.0
O B:HOH166 4.8 18.9 1.0
C B:LYS136 4.9 18.6 1.0
C B:HIS71 4.9 19.6 1.0
CA B:HIS63 4.9 15.7 1.0
N B:ASP83 4.9 12.0 1.0
N B:HIS71 4.9 18.6 1.0

Zinc binding site 3 out of 10 in 3gzo

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Zinc binding site 3 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn155

b:29.3
occ:1.00
ND1 C:HIS80 2.0 21.6 1.0
OD1 C:ASP83 2.1 24.6 1.0
ND1 C:HIS71 2.2 28.7 1.0
ND1 C:HIS63 2.3 31.1 1.0
CG C:ASP83 2.8 26.3 1.0
OD2 C:ASP83 2.8 28.2 1.0
CE1 C:HIS80 3.0 27.5 1.0
CG C:HIS80 3.0 30.1 1.0
CE1 C:HIS71 3.2 29.4 1.0
CG C:HIS71 3.2 30.7 1.0
CG C:HIS63 3.2 29.8 1.0
CB C:HIS80 3.4 27.1 1.0
CB C:HIS63 3.4 30.4 1.0
CE1 C:HIS63 3.4 31.6 1.0
CB C:HIS71 3.5 29.7 1.0
O C:LYS136 3.8 37.2 1.0
CA C:HIS71 3.8 31.2 1.0
NE2 C:HIS80 4.1 29.1 1.0
CD2 C:HIS80 4.1 29.2 1.0
CB C:ASP83 4.2 24.9 1.0
NE2 C:HIS71 4.3 34.1 1.0
CD2 C:HIS71 4.3 32.1 1.0
CD2 C:HIS63 4.4 28.5 1.0
NE2 C:HIS63 4.5 32.5 1.0
N C:HIS80 4.6 30.6 1.0
CA C:HIS80 4.6 29.2 1.0
N C:GLY72 4.6 29.4 1.0
O C:HOH1319 4.7 30.2 1.0
CA C:ASP83 4.7 23.3 1.0
C C:HIS71 4.8 29.2 1.0
C C:LYS136 4.8 36.9 1.0
N C:HIS71 4.8 31.7 1.0
CA C:HIS63 4.9 26.7 1.0
N C:ASP83 4.9 25.4 1.0
O C:GLY72 5.0 31.6 1.0

Zinc binding site 4 out of 10 in 3gzo

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Zinc binding site 4 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn155

b:17.9
occ:1.00
OD1 D:ASP83 2.1 13.4 1.0
ND1 D:HIS71 2.1 16.0 1.0
ND1 D:HIS80 2.1 16.3 1.0
ND1 D:HIS63 2.2 16.3 1.0
CG D:ASP83 2.8 16.1 1.0
OD2 D:ASP83 2.9 16.8 1.0
CE1 D:HIS80 3.0 19.2 1.0
CE1 D:HIS71 3.0 15.3 1.0
CE1 D:HIS63 3.1 17.4 1.0
CG D:HIS63 3.1 17.3 1.0
CG D:HIS80 3.1 18.6 1.0
CG D:HIS71 3.1 15.3 1.0
CB D:HIS63 3.4 14.9 1.0
CB D:HIS71 3.5 17.1 1.0
CB D:HIS80 3.5 16.5 1.0
O D:LYS136 3.8 16.5 1.0
CA D:HIS71 3.9 17.8 1.0
NE2 D:HIS80 4.1 18.6 1.0
NE2 D:HIS71 4.1 14.5 1.0
CB D:ASP83 4.2 13.2 1.0
CD2 D:HIS80 4.2 17.7 1.0
NE2 D:HIS63 4.2 19.9 1.0
CD2 D:HIS71 4.2 16.2 1.0
CD2 D:HIS63 4.3 18.3 1.0
N D:HIS80 4.7 16.4 1.0
N D:GLY72 4.7 13.7 1.0
CA D:HIS80 4.7 16.1 1.0
CA D:ASP83 4.7 16.1 1.0
C D:LYS136 4.8 19.3 1.0
O D:HOH170 4.8 17.6 1.0
C D:HIS71 4.8 17.6 1.0
N D:HIS71 4.9 18.1 1.0
CA D:HIS63 5.0 17.2 1.0
N D:ASP83 5.0 14.6 1.0

Zinc binding site 5 out of 10 in 3gzo

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Zinc binding site 5 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn155

b:17.6
occ:1.00
OD1 E:ASP83 2.0 13.7 1.0
ND1 E:HIS71 2.1 18.6 1.0
ND1 E:HIS63 2.1 16.2 1.0
ND1 E:HIS80 2.1 16.0 1.0
CG E:ASP83 2.7 18.4 1.0
OD2 E:ASP83 2.9 17.0 1.0
CE1 E:HIS80 3.0 14.9 1.0
CE1 E:HIS71 3.0 16.6 1.0
CE1 E:HIS63 3.0 18.5 1.0
CG E:HIS80 3.1 16.6 1.0
CG E:HIS63 3.1 18.0 1.0
CG E:HIS71 3.1 19.1 1.0
CB E:HIS63 3.4 14.0 1.0
CB E:HIS71 3.4 16.6 1.0
CB E:HIS80 3.5 15.2 1.0
O E:LYS136 3.7 19.2 1.0
CA E:HIS71 3.8 19.2 1.0
NE2 E:HIS80 4.0 17.8 1.0
CD2 E:HIS80 4.1 17.9 1.0
NE2 E:HIS63 4.2 17.7 1.0
NE2 E:HIS71 4.2 18.2 1.0
CB E:ASP83 4.2 14.7 1.0
CD2 E:HIS63 4.2 16.5 1.0
CD2 E:HIS71 4.2 16.4 1.0
CA E:ASP83 4.7 17.1 1.0
N E:HIS80 4.7 18.8 1.0
C E:LYS136 4.7 23.6 1.0
CA E:HIS80 4.7 15.7 1.0
N E:GLY72 4.7 15.5 1.0
C E:HIS71 4.8 18.5 1.0
N E:HIS71 4.9 17.5 1.0
CA E:HIS63 4.9 14.7 1.0
O E:HOH163 4.9 19.3 1.0
CD2 E:HIS46 4.9 17.9 1.0
N E:ASP83 5.0 19.7 1.0

Zinc binding site 6 out of 10 in 3gzo

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Zinc binding site 6 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn155

b:15.4
occ:1.00
OD1 F:ASP83 1.9 14.5 1.0
ND1 F:HIS63 2.0 15.2 1.0
ND1 F:HIS80 2.2 17.9 1.0
ND1 F:HIS71 2.2 16.5 1.0
CG F:ASP83 2.7 15.2 1.0
OD2 F:ASP83 2.9 13.2 1.0
CE1 F:HIS63 3.0 15.4 1.0
CG F:HIS63 3.0 13.7 1.0
CE1 F:HIS80 3.1 17.4 1.0
CE1 F:HIS71 3.1 15.8 1.0
CG F:HIS80 3.2 15.3 1.0
CG F:HIS71 3.2 17.8 1.0
CB F:HIS63 3.4 15.6 1.0
CB F:HIS80 3.5 14.8 1.0
CB F:HIS71 3.6 14.9 1.0
O F:LYS136 3.7 20.0 1.0
CA F:HIS71 3.9 15.3 1.0
NE2 F:HIS63 4.1 14.7 1.0
CD2 F:HIS63 4.1 15.2 1.0
CB F:ASP83 4.1 13.9 1.0
NE2 F:HIS80 4.2 18.3 1.0
CD2 F:HIS80 4.3 15.2 1.0
NE2 F:HIS71 4.3 14.2 1.0
CD2 F:HIS71 4.4 14.9 1.0
CA F:ASP83 4.6 13.7 1.0
N F:HIS80 4.7 12.6 1.0
C F:LYS136 4.7 18.5 1.0
CA F:HIS80 4.7 15.4 1.0
N F:GLY72 4.8 16.4 1.0
N F:ASP83 4.9 14.5 1.0
C F:HIS71 4.9 18.6 1.0
N F:HIS71 4.9 18.0 1.0
O F:HOH166 4.9 18.3 1.0
CA F:HIS63 4.9 13.7 1.0

Zinc binding site 7 out of 10 in 3gzo

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Zinc binding site 7 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn155

b:18.7
occ:1.00
OD1 G:ASP83 2.0 15.9 1.0
ND1 G:HIS80 2.1 15.9 1.0
ND1 G:HIS71 2.1 16.7 1.0
ND1 G:HIS63 2.2 18.1 1.0
CG G:ASP83 2.7 16.4 1.0
OD2 G:ASP83 2.8 18.3 1.0
CE1 G:HIS71 3.0 17.2 1.0
CE1 G:HIS80 3.0 18.7 1.0
CG G:HIS80 3.0 18.3 1.0
CG G:HIS63 3.1 19.2 1.0
CG G:HIS71 3.2 17.2 1.0
CE1 G:HIS63 3.2 18.9 1.0
CB G:HIS63 3.3 18.1 1.0
CB G:HIS80 3.4 16.6 1.0
CB G:HIS71 3.5 18.9 1.0
O G:LYS136 3.9 21.7 1.0
CA G:HIS71 3.9 17.4 1.0
NE2 G:HIS80 4.1 22.3 1.0
CB G:ASP83 4.1 14.9 1.0
CD2 G:HIS80 4.1 18.6 1.0
NE2 G:HIS71 4.2 19.9 1.0
CD2 G:HIS71 4.2 18.4 1.0
CD2 G:HIS63 4.3 19.6 1.0
NE2 G:HIS63 4.3 20.7 1.0
CA G:ASP83 4.7 15.8 1.0
CA G:HIS80 4.7 19.0 1.0
O G:HOH445 4.7 25.0 1.0
N G:HIS80 4.7 19.2 1.0
N G:GLY72 4.7 20.4 1.0
CA G:HIS63 4.9 16.4 1.0
N G:ASP83 4.9 16.4 1.0
CD2 G:HIS46 4.9 18.6 1.0
C G:HIS71 4.9 19.3 1.0
C G:LYS136 4.9 21.1 1.0
N G:HIS71 4.9 16.3 1.0

Zinc binding site 8 out of 10 in 3gzo

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Zinc binding site 8 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn155

b:17.6
occ:1.00
OD1 H:ASP83 2.0 15.7 1.0
ND1 H:HIS80 2.0 14.6 1.0
ND1 H:HIS63 2.1 16.7 1.0
ND1 H:HIS71 2.1 16.8 1.0
CG H:ASP83 2.7 19.2 1.0
OD2 H:ASP83 2.8 14.9 1.0
CE1 H:HIS80 2.9 15.8 1.0
CE1 H:HIS63 3.0 18.2 1.0
CE1 H:HIS71 3.0 14.5 1.0
CG H:HIS63 3.1 18.5 1.0
CG H:HIS80 3.1 19.1 1.0
CG H:HIS71 3.1 18.6 1.0
CB H:HIS63 3.4 15.4 1.0
CB H:HIS71 3.5 16.0 1.0
CB H:HIS80 3.5 17.6 1.0
O H:LYS136 3.8 18.7 1.0
CA H:HIS71 3.9 16.6 1.0
NE2 H:HIS80 4.0 21.4 1.0
CD2 H:HIS80 4.1 18.0 1.0
NE2 H:HIS63 4.1 18.1 1.0
CB H:ASP83 4.2 16.1 1.0
NE2 H:HIS71 4.2 16.9 1.0
CD2 H:HIS63 4.2 19.7 1.0
CD2 H:HIS71 4.2 16.5 1.0
N H:HIS80 4.6 16.0 1.0
N H:GLY72 4.7 20.6 1.0
CA H:ASP83 4.7 17.8 1.0
CA H:HIS80 4.7 17.4 1.0
C H:LYS136 4.8 23.4 1.0
C H:HIS71 4.8 20.5 1.0
N H:HIS71 4.9 19.4 1.0
CA H:HIS63 4.9 15.4 1.0
N H:ASP83 5.0 17.2 1.0
O H:HOH258 5.0 17.0 1.0

Zinc binding site 9 out of 10 in 3gzo

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Zinc binding site 9 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn155

b:33.5
occ:1.00
OD1 I:ASP83 2.0 31.3 1.0
ND1 I:HIS63 2.1 28.1 1.0
ND1 I:HIS80 2.1 30.5 1.0
ND1 I:HIS71 2.4 35.8 1.0
CG I:ASP83 2.7 34.1 1.0
OD2 I:ASP83 2.8 33.0 1.0
CE1 I:HIS80 3.0 31.8 1.0
CE1 I:HIS63 3.0 34.2 1.0
CG I:HIS63 3.1 30.5 1.0
CG I:HIS80 3.1 31.8 1.0
CE1 I:HIS71 3.3 35.2 1.0
CG I:HIS71 3.3 40.2 1.0
CB I:HIS63 3.4 26.0 1.0
CB I:HIS80 3.6 33.0 1.0
CB I:HIS71 3.6 35.1 1.0
O I:LYS136 3.8 38.4 1.0
CA I:HIS71 3.9 36.0 1.0
NE2 I:HIS80 4.1 34.3 1.0
CB I:ASP83 4.2 29.5 1.0
NE2 I:HIS63 4.2 33.8 1.0
CD2 I:HIS80 4.2 34.0 1.0
CD2 I:HIS63 4.2 30.8 1.0
NE2 I:HIS71 4.3 37.9 1.0
CD2 I:HIS71 4.4 39.9 1.0
CA I:ASP83 4.7 31.2 1.0
N I:GLY72 4.7 37.0 1.0
N I:HIS80 4.8 37.4 1.0
CD2 I:HIS46 4.8 25.9 1.0
CA I:HIS80 4.8 33.2 1.0
C I:LYS136 4.8 38.9 1.0
O I:HOH337 4.8 28.4 1.0
C I:HIS71 4.9 39.2 1.0
N I:HIS71 4.9 35.9 1.0
CA I:HIS63 5.0 29.4 1.0
N I:ASP83 5.0 28.5 1.0

Zinc binding site 10 out of 10 in 3gzo

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Zinc binding site 10 out of 10 in the Human SOD1 G93A Variant


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 10 of Human SOD1 G93A Variant within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn155

b:21.6
occ:1.00
OD1 J:ASP83 2.0 17.7 1.0
ND1 J:HIS80 2.0 21.4 1.0
ND1 J:HIS63 2.2 20.1 1.0
ND1 J:HIS71 2.2 16.5 1.0
CG J:ASP83 2.8 19.8 1.0
CE1 J:HIS80 2.9 18.1 1.0
OD2 J:ASP83 2.9 21.0 1.0
CG J:HIS80 3.1 23.4 1.0
CE1 J:HIS71 3.1 18.2 1.0
CG J:HIS63 3.1 20.8 1.0
CE1 J:HIS63 3.2 23.4 1.0
CG J:HIS71 3.3 20.2 1.0
CB J:HIS63 3.3 20.8 1.0
CB J:HIS80 3.5 20.6 1.0
CB J:HIS71 3.6 18.4 1.0
O J:LYS136 3.8 21.4 1.0
CA J:HIS71 4.0 22.5 1.0
NE2 J:HIS80 4.0 21.1 1.0
CD2 J:HIS80 4.1 21.0 1.0
CB J:ASP83 4.2 17.9 1.0
NE2 J:HIS71 4.2 21.4 1.0
CD2 J:HIS63 4.3 23.3 1.0
NE2 J:HIS63 4.3 23.7 1.0
CD2 J:HIS71 4.3 18.3 1.0
N J:HIS80 4.6 22.7 1.0
CA J:HIS80 4.7 22.5 1.0
CA J:ASP83 4.7 20.1 1.0
N J:GLY72 4.7 22.4 1.0
C J:LYS136 4.8 21.2 1.0
O J:HOH256 4.9 28.0 1.0
CA J:HIS63 4.9 23.1 1.0
C J:HIS71 4.9 20.6 1.0
N J:ASP83 4.9 20.6 1.0
CD2 J:HIS46 5.0 21.1 1.0
N J:HIS71 5.0 23.4 1.0

Reference:

A.Galaleldeen, R.W.Strange, L.J.Whitson, S.V.Antonyuk, N.Narayana, A.B.Taylor, J.P.Schuermann, S.P.Holloway, S.S.Hasnain, P.J.Hart. Structural and Biophysical Properties of Metal-Free Pathogenic SOD1 Mutants A4V and G93A. Arch.Biochem.Biophys. V. 492 40 2009.
ISSN: ISSN 0003-9861
PubMed: 19800308
DOI: 10.1016/J.ABB.2009.09.020
Page generated: Wed Dec 16 04:22:15 2020

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