Zinc in PDB 6spi: A4V Mutant of Human SOD1 with Ebselen Derivative 4

Enzymatic activity of A4V Mutant of Human SOD1 with Ebselen Derivative 4

All present enzymatic activity of A4V Mutant of Human SOD1 with Ebselen Derivative 4:
1.15.1.1;

Protein crystallography data

The structure of A4V Mutant of Human SOD1 with Ebselen Derivative 4, PDB code: 6spi was solved by V.Chantadul, K.Amporndanai, G.Wright, S.Antonyuk, S.Hasnain, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 58.54 / 2.80
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.526, 194.671, 146.526, 90.00, 93.44, 90.00
R / Rfree (%) 21.3 / 24.1

Other elements in 6spi:

The structure of A4V Mutant of Human SOD1 with Ebselen Derivative 4 also contains other interesting chemical elements:

Chlorine (Cl) 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 with Ebselen Derivative 4 (pdb code 6spi). 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 with Ebselen Derivative 4, PDB code: 6spi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Zinc binding site 1 out of 12 in 6spi

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Zinc binding site 1 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn202

b:21.7
occ:1.00
OD1 A:ASP83 1.8 22.7 1.0
ND1 A:HIS80 2.0 19.8 1.0
ND1 A:HIS71 2.0 26.4 1.0
ND1 A:HIS63 2.0 18.0 1.0
CG A:ASP83 2.6 22.9 1.0
OD2 A:ASP83 2.7 22.7 1.0
CE1 A:HIS80 2.9 19.3 1.0
CE1 A:HIS71 2.9 28.6 1.0
CE1 A:HIS63 3.0 17.1 1.0
CG A:HIS80 3.0 19.5 1.0
CG A:HIS63 3.0 17.5 1.0
CG A:HIS71 3.1 26.2 1.0
CB A:HIS63 3.3 18.0 1.0
CB A:HIS80 3.4 20.4 1.0
CB A:HIS71 3.5 26.7 1.0
O A:LYS136 3.9 30.7 1.0
CA A:HIS71 3.9 25.5 1.0
NE2 A:HIS80 4.0 20.5 1.0
CB A:ASP83 4.0 22.1 1.0
CD2 A:HIS80 4.1 18.9 1.0
NE2 A:HIS71 4.1 28.3 1.0
NE2 A:HIS63 4.1 16.0 1.0
CD2 A:HIS63 4.1 16.3 1.0
CD2 A:HIS71 4.2 26.6 1.0
CA A:ASP83 4.6 21.4 1.0
N A:HIS80 4.6 23.6 1.0
CA A:HIS80 4.7 21.8 1.0
N A:GLY72 4.7 25.5 1.0
CA A:HIS63 4.9 19.3 1.0
C A:HIS71 4.9 24.6 1.0
C A:LYS136 4.9 29.1 1.0
N A:ASP83 4.9 20.2 1.0
CD2 A:HIS46 4.9 19.9 1.0
N A:HIS71 5.0 26.0 1.0

Zinc binding site 2 out of 12 in 6spi

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Zinc binding site 2 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn202

b:24.2
occ:1.00
OD1 B:ASP83 1.8 24.8 1.0
ND1 B:HIS80 1.9 22.3 1.0
ND1 B:HIS71 2.0 27.4 1.0
ND1 B:HIS63 2.0 20.5 1.0
CG B:ASP83 2.6 25.4 1.0
OD2 B:ASP83 2.7 25.1 1.0
CE1 B:HIS80 2.8 21.8 1.0
CE1 B:HIS71 2.9 29.2 1.0
CG B:HIS80 3.0 22.9 1.0
CE1 B:HIS63 3.0 19.9 1.0
CG B:HIS63 3.0 19.5 1.0
CG B:HIS71 3.1 27.4 1.0
CB B:HIS63 3.3 19.5 1.0
CB B:HIS80 3.4 23.6 1.0
CB B:HIS71 3.5 27.7 1.0
O B:LYS136 3.8 28.6 1.0
CA B:HIS71 3.9 26.3 1.0
NE2 B:HIS80 4.0 22.8 1.0
CD2 B:HIS80 4.0 21.8 1.0
CB B:ASP83 4.0 24.9 1.0
NE2 B:HIS71 4.1 30.2 1.0
NE2 B:HIS63 4.1 18.8 1.0
CD2 B:HIS63 4.1 18.9 1.0
CD2 B:HIS71 4.2 28.4 1.0
CA B:ASP83 4.6 26.0 1.0
N B:HIS80 4.6 25.6 1.0
CA B:HIS80 4.6 23.5 1.0
N B:GLY72 4.7 28.3 1.0
C B:HIS71 4.8 27.2 1.0
CA B:HIS63 4.9 21.3 1.0
C B:LYS136 4.9 28.3 1.0
N B:HIS71 4.9 25.5 1.0
N B:ASP83 4.9 24.8 1.0
CD2 B:HIS46 5.0 28.0 1.0

Zinc binding site 3 out of 12 in 6spi

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Zinc binding site 3 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn202

b:21.2
occ:1.00
OD1 C:ASP83 1.8 21.2 1.0
ND1 C:HIS80 2.0 22.2 1.0
ND1 C:HIS63 2.0 20.4 1.0
ND1 C:HIS71 2.0 22.7 1.0
CG C:ASP83 2.6 21.1 1.0
OD2 C:ASP83 2.8 20.4 1.0
CE1 C:HIS80 2.9 21.6 1.0
CE1 C:HIS71 2.9 23.0 1.0
CE1 C:HIS63 2.9 20.3 1.0
CG C:HIS63 3.0 19.4 1.0
CG C:HIS80 3.0 22.6 1.0
CG C:HIS71 3.1 23.1 1.0
CB C:HIS63 3.3 18.5 1.0
CB C:HIS80 3.4 22.7 1.0
CB C:HIS71 3.5 24.1 1.0
O C:LYS136 3.8 32.1 1.0
CA C:HIS71 4.0 26.9 1.0
NE2 C:HIS80 4.0 21.5 1.0
CB C:ASP83 4.0 21.2 1.0
NE2 C:HIS63 4.1 20.3 1.0
CD2 C:HIS80 4.1 22.0 1.0
CD2 C:HIS63 4.1 19.6 1.0
NE2 C:HIS71 4.1 23.4 1.0
CD2 C:HIS71 4.2 22.6 1.0
CA C:ASP83 4.6 22.8 1.0
CA C:HIS80 4.7 25.6 1.0
N C:HIS80 4.7 26.2 1.0
N C:GLY72 4.8 27.5 1.0
CA C:HIS63 4.8 19.2 1.0
C C:LYS136 4.9 32.8 1.0
C C:HIS71 4.9 28.9 1.0
CD2 C:HIS46 4.9 23.3 1.0
N C:ASP83 4.9 22.0 1.0
N C:HIS71 5.0 26.5 1.0

Zinc binding site 4 out of 12 in 6spi

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


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn202

b:27.3
occ:1.00
OD1 D:ASP83 1.8 29.3 1.0
ND1 D:HIS80 2.0 28.6 1.0
ND1 D:HIS71 2.0 31.7 1.0
ND1 D:HIS63 2.0 28.9 1.0
CG D:ASP83 2.6 29.2 1.0
OD2 D:ASP83 2.7 28.5 1.0
CE1 D:HIS80 2.9 29.6 1.0
CE1 D:HIS71 2.9 33.8 1.0
CE1 D:HIS63 3.0 31.2 1.0
CG D:HIS80 3.0 27.4 1.0
CG D:HIS63 3.0 27.8 1.0
CG D:HIS71 3.1 32.4 1.0
CB D:HIS63 3.4 27.9 1.0
CB D:HIS80 3.4 27.7 1.0
CB D:HIS71 3.5 31.0 1.0
O D:LYS136 3.8 40.9 1.0
CA D:HIS71 3.9 32.5 1.0
NE2 D:HIS80 4.0 30.2 1.0
CB D:ASP83 4.0 26.9 1.0
CD2 D:HIS80 4.1 27.3 1.0
NE2 D:HIS71 4.1 36.1 1.0
NE2 D:HIS63 4.1 28.0 1.0
CD2 D:HIS63 4.2 27.2 1.0
CD2 D:HIS71 4.2 34.5 1.0
CA D:ASP83 4.6 27.1 1.0
N D:HIS80 4.7 33.4 1.0
CA D:HIS80 4.7 30.2 1.0
N D:GLY72 4.7 35.2 1.0
O D:HOH310 4.8 12.3 1.0
C D:HIS71 4.9 36.0 1.0
C D:LYS136 4.9 41.0 1.0
CA D:HIS63 4.9 28.8 1.0
N D:ASP83 4.9 28.2 1.0
CD2 D:HIS46 4.9 23.0 1.0
N D:HIS71 4.9 30.9 1.0

Zinc binding site 5 out of 12 in 6spi

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Zinc binding site 5 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn202

b:22.2
occ:1.00
OD1 E:ASP83 1.8 21.2 1.0
ND1 E:HIS63 2.0 20.7 1.0
ND1 E:HIS80 2.0 21.9 1.0
ND1 E:HIS71 2.0 22.3 1.0
CG E:ASP83 2.6 20.1 1.0
OD2 E:ASP83 2.7 21.4 1.0
CE1 E:HIS80 2.9 22.1 1.0
CE1 E:HIS71 2.9 22.5 1.0
CE1 E:HIS63 2.9 20.8 1.0
CG E:HIS63 3.0 21.6 1.0
CG E:HIS80 3.0 21.8 1.0
CG E:HIS71 3.1 22.1 1.0
CB E:HIS63 3.3 22.4 1.0
CB E:HIS80 3.4 21.7 1.0
CB E:HIS71 3.5 22.0 1.0
O E:LYS136 3.9 26.6 1.0
CA E:HIS71 4.0 23.6 1.0
CB E:ASP83 4.0 19.1 1.0
NE2 E:HIS80 4.0 22.8 1.0
NE2 E:HIS63 4.1 22.2 1.0
NE2 E:HIS71 4.1 23.1 1.0
CD2 E:HIS80 4.1 22.4 1.0
CD2 E:HIS63 4.1 21.6 1.0
CD2 E:HIS71 4.2 22.6 1.0
CA E:ASP83 4.6 19.9 1.0
CA E:HIS80 4.7 22.6 1.0
N E:HIS80 4.7 24.1 1.0
N E:GLY72 4.8 27.2 1.0
CA E:HIS63 4.8 23.4 1.0
N E:ASP83 4.9 20.8 1.0
CD2 E:HIS46 4.9 22.4 1.0
C E:LYS136 4.9 27.5 1.0
C E:HIS71 4.9 26.4 1.0

Zinc binding site 6 out of 12 in 6spi

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Zinc binding site 6 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:25.7
occ:1.00
OD1 F:ASP83 1.8 27.5 1.0
ND1 F:HIS80 1.9 27.7 1.0
ND1 F:HIS63 2.0 25.0 1.0
ND1 F:HIS71 2.0 26.1 1.0
CG F:ASP83 2.6 26.5 1.0
OD2 F:ASP83 2.7 25.4 1.0
CE1 F:HIS80 2.8 27.6 1.0
CG F:HIS80 3.0 28.3 1.0
CE1 F:HIS71 3.0 25.3 1.0
CE1 F:HIS63 3.0 25.7 1.0
CG F:HIS63 3.0 24.9 1.0
CG F:HIS71 3.1 26.1 1.0
CB F:HIS63 3.3 25.7 1.0
CB F:HIS80 3.4 28.1 1.0
CB F:HIS71 3.5 26.9 1.0
O F:LYS136 3.8 38.5 1.0
CA F:HIS71 3.9 28.1 1.0
NE2 F:HIS80 3.9 28.1 1.0
CD2 F:HIS80 4.0 28.6 1.0
CB F:ASP83 4.1 24.3 1.0
NE2 F:HIS63 4.1 25.6 1.0
NE2 F:HIS71 4.1 26.6 1.0
CD2 F:HIS63 4.1 24.8 1.0
CD2 F:HIS71 4.2 25.9 1.0
CA F:ASP83 4.6 25.1 1.0
CA F:HIS80 4.6 30.5 1.0
N F:HIS80 4.6 31.7 1.0
N F:GLY72 4.8 30.1 1.0
CA F:HIS63 4.8 26.5 1.0
C F:LYS136 4.9 35.0 1.0
C F:HIS71 4.9 31.3 1.0
N F:ASP83 4.9 25.8 1.0
N F:HIS71 4.9 26.6 1.0
CD2 F:HIS46 5.0 26.3 1.0

Zinc binding site 7 out of 12 in 6spi

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Zinc binding site 7 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn202

b:22.5
occ:1.00
OD1 G:ASP83 1.9 22.7 1.0
ND1 G:HIS80 1.9 20.4 1.0
ND1 G:HIS63 2.0 20.1 1.0
ND1 G:HIS71 2.0 25.9 1.0
CG G:ASP83 2.6 21.9 1.0
OD2 G:ASP83 2.7 21.6 1.0
CE1 G:HIS80 2.8 19.9 1.0
CE1 G:HIS71 3.0 26.1 1.0
CG G:HIS80 3.0 20.5 1.0
CE1 G:HIS63 3.0 19.7 1.0
CG G:HIS63 3.0 20.7 1.0
CG G:HIS71 3.1 25.5 1.0
CB G:HIS63 3.3 21.1 1.0
CB G:HIS80 3.4 20.7 1.0
CB G:HIS71 3.5 25.2 1.0
O G:LYS136 3.8 32.9 1.0
CA G:HIS71 3.9 25.9 1.0
NE2 G:HIS80 3.9 20.3 1.0
CD2 G:HIS80 4.0 20.6 1.0
CB G:ASP83 4.1 20.8 1.0
NE2 G:HIS71 4.1 26.2 1.0
NE2 G:HIS63 4.1 20.9 1.0
CD2 G:HIS63 4.2 19.9 1.0
CD2 G:HIS71 4.2 25.6 1.0
N G:HIS80 4.6 23.4 1.0
CA G:ASP83 4.6 20.9 1.0
CA G:HIS80 4.6 21.7 1.0
N G:GLY72 4.7 30.5 1.0
C G:HIS71 4.9 27.9 1.0
CA G:HIS63 4.9 21.6 1.0
C G:LYS136 4.9 30.6 1.0
N G:HIS71 4.9 25.5 1.0
N G:ASP83 5.0 20.1 1.0
CD2 G:HIS46 5.0 27.1 1.0

Zinc binding site 8 out of 12 in 6spi

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Zinc binding site 8 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn202

b:24.8
occ:1.00
OD1 H:ASP83 1.8 28.4 1.0
ND1 H:HIS80 2.0 23.2 1.0
ND1 H:HIS71 2.0 28.3 1.0
ND1 H:HIS63 2.0 23.6 1.0
CG H:ASP83 2.6 27.9 1.0
OD2 H:ASP83 2.7 28.4 1.0
CE1 H:HIS80 2.9 22.4 1.0
CE1 H:HIS71 2.9 29.1 1.0
CE1 H:HIS63 3.0 23.4 1.0
CG H:HIS80 3.0 24.3 1.0
CG H:HIS63 3.0 22.7 1.0
CG H:HIS71 3.1 28.1 1.0
CB H:HIS63 3.4 22.8 1.0
CB H:HIS80 3.4 26.9 1.0
CB H:HIS71 3.5 29.0 1.0
O H:LYS136 3.8 23.6 1.0
CA H:HIS71 3.9 29.9 1.0
NE2 H:HIS80 4.0 23.0 1.0
CB H:ASP83 4.0 25.9 1.0
NE2 H:HIS71 4.0 28.9 1.0
CD2 H:HIS80 4.1 23.5 1.0
NE2 H:HIS63 4.1 23.2 1.0
CD2 H:HIS71 4.1 28.7 1.0
CD2 H:HIS63 4.1 22.4 1.0
CA H:ASP83 4.6 26.8 1.0
N H:HIS80 4.7 32.3 1.0
CA H:HIS80 4.7 28.9 1.0
N H:GLY72 4.7 28.0 1.0
C H:HIS71 4.9 28.7 1.0
C H:LYS136 4.9 26.2 1.0
CA H:HIS63 4.9 23.6 1.0
CD2 H:HIS46 4.9 33.2 1.0
N H:ASP83 4.9 27.0 1.0
N H:HIS71 4.9 30.8 1.0

Zinc binding site 9 out of 12 in 6spi

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Zinc binding site 9 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:21.1
occ:1.00
OD1 I:ASP83 1.8 21.8 1.0
ND1 I:HIS80 2.0 19.4 1.0
ND1 I:HIS71 2.0 25.0 1.0
ND1 I:HIS63 2.0 20.4 1.0
CG I:ASP83 2.5 21.4 1.0
OD2 I:ASP83 2.7 22.6 1.0
CE1 I:HIS80 2.9 19.4 1.0
CE1 I:HIS71 2.9 24.3 1.0
CG I:HIS80 3.0 18.9 1.0
CE1 I:HIS63 3.0 20.2 1.0
CG I:HIS63 3.0 19.9 1.0
CG I:HIS71 3.1 25.8 1.0
CB I:HIS63 3.3 20.9 1.0
CB I:HIS80 3.4 19.2 1.0
CB I:HIS71 3.5 24.3 1.0
O I:LYS136 3.9 22.9 1.0
CA I:HIS71 3.9 24.3 1.0
CB I:ASP83 4.0 20.0 1.0
NE2 I:HIS80 4.0 19.3 1.0
CD2 I:HIS80 4.1 18.7 1.0
NE2 I:HIS71 4.1 26.1 1.0
NE2 I:HIS63 4.1 19.9 1.0
CD2 I:HIS63 4.1 19.8 1.0
CD2 I:HIS71 4.1 26.9 1.0
CA I:ASP83 4.6 19.4 1.0
N I:HIS80 4.6 22.1 1.0
CA I:HIS80 4.6 21.1 1.0
N I:GLY72 4.7 26.2 1.0
C I:HIS71 4.8 25.1 1.0
CA I:HIS63 4.9 22.9 1.0
N I:ASP83 4.9 18.2 1.0
C I:LYS136 4.9 23.7 1.0
CD2 I:HIS46 4.9 20.6 1.0
N I:HIS71 5.0 26.7 1.0
O I:GLY72 5.0 31.3 1.0

Zinc binding site 10 out of 12 in 6spi

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Zinc binding site 10 out of 12 in the A4V Mutant of Human SOD1 with Ebselen Derivative 4


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 with Ebselen Derivative 4 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn202

b:20.5
occ:1.00
OD1 J:ASP83 1.8 19.6 1.0
ND1 J:HIS80 1.9 20.6 1.0
ND1 J:HIS63 2.0 19.7 1.0
ND1 J:HIS71 2.1 23.6 1.0
CG J:ASP83 2.6 19.3 1.0
OD2 J:ASP83 2.7 18.7 1.0
CE1 J:HIS80 2.8 21.6 1.0
CG J:HIS80 2.9 21.1 1.0
CG J:HIS63 3.0 20.0 1.0
CE1 J:HIS71 3.0 24.8 1.0
CE1 J:HIS63 3.0 19.6 1.0
CG J:HIS71 3.2 23.6 1.0
CB J:HIS63 3.3 20.1 1.0
CB J:HIS80 3.3 21.9 1.0
CB J:HIS71 3.5 23.1 1.0
O J:LYS136 3.9 34.0 1.0
NE2 J:HIS80 3.9 21.7 1.0
CA J:HIS71 3.9 24.1 1.0
CD2 J:HIS80 4.0 20.3 1.0
CB J:ASP83 4.0 18.4 1.0
CD2 J:HIS63 4.1 19.8 1.0
NE2 J:HIS63 4.1 19.6 1.0
NE2 J:HIS71 4.2 26.9 1.0
CD2 J:HIS71 4.2 25.7 1.0
CA J:HIS80 4.6 21.9 1.0
N J:HIS80 4.6 23.0 1.0
CA J:ASP83 4.6 18.0 1.0
N J:GLY72 4.8 25.5 1.0
CA J:HIS63 4.8 20.7 1.0
N J:ASP83 4.9 18.0 1.0
C J:HIS71 4.9 24.7 1.0
C J:LYS136 4.9 34.3 1.0
N J:HIS71 5.0 25.7 1.0

Reference:

V.Chantadul, G.S.A.Wright, K.Amporndanai, M.Shahid, S.V.Antonyuk, G.Washbourn, M.Rogers, N.Roberts, M.Pye, P.M.O'neill, S.S.Hasnain. Ebselen As Template For Stabilization of A4V Mutant Dimer For Motor Neuron Disease Therapy. Commun Biol V. 3 97 2020.
ISSN: ESSN 2399-3642
PubMed: 32139772
DOI: 10.1038/S42003-020-0826-3
Page generated: Wed Dec 16 12:49:23 2020

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