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Zinc in PDB 6sph: A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group

Enzymatic activity of A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group

All present enzymatic activity of A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group:
1.15.1.1;

Protein crystallography data

The structure of A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group, PDB code: 6sph was solved by M.Shahid, 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) 43.00 / 2.25
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.313, 195.237, 75.348, 90.00, 97.86, 90.00
R / Rfree (%) 18.6 / 22.2

Zinc Binding Sites:

The binding sites of Zinc atom in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group (pdb code 6sph). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group, PDB code: 6sph:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 6sph

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Zinc binding site 1 out of 6 in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group


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 Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:12.9
occ:1.00
 OD1 A:ASP83 1.9 12.8 1.0
ND1 A:HIS80 1.9 13.9 1.0
ND1 A:HIS63 2.0 14.0 1.0
ND1 A:HIS71 2.2 16.8 1.0
CG A:ASP83 2.7 13.4 1.0
OD2 A:ASP83 2.8 13.1 1.0
CE1 A:HIS80 2.8 13.8 1.0
CG A:HIS80 3.0 13.9 1.0
CE1 A:HIS63 3.0 13.9 1.0
CG A:HIS63 3.0 13.8 1.0
CE1 A:HIS71 3.1 16.9 1.0
CG A:HIS71 3.2 16.6 1.0
CB A:HIS63 3.3 13.7 1.0
CB A:HIS80 3.4 14.5 1.0
CB A:HIS71 3.6 16.5 1.0
O A:LYS136 3.8 15.5 1.0
CA A:HIS71 3.9 17.0 1.0
NE2 A:HIS80 4.0 13.6 1.0
CD2 A:HIS80 4.0 13.5 1.0
NE2 A:HIS63 4.1 13.7 1.0
CD2 A:HIS63 4.1 13.6 1.0
CB A:ASP83 4.1 13.6 1.0
NE2 A:HIS71 4.2 16.9 1.0
CD2 A:HIS71 4.3 16.7 1.0
O A:HOH343 4.7 29.4 1.0
CA A:ASP83 4.7 14.2 1.0
CA A:HIS80 4.7 14.7 1.0
N A:HIS80 4.7 15.5 1.0
N A:GLY72 4.8 16.6 1.0
C A:LYS136 4.8 16.0 1.0
CA A:HIS63 4.8 13.8 1.0
C A:HIS71 4.9 16.6 1.0
N A:HIS71 4.9 17.6 1.0
CD2 A:HIS46 4.9 16.3 1.0
N A:ASP83 4.9 14.0 1.0

Zinc binding site 2 out of 6 in 6sph

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Zinc binding site 2 out of 6 in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group


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 Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:14.8
occ:1.00
 ND1 C:HIS80 1.9 14.8 1.0
OD1 C:ASP83 1.9 13.8 1.0
ND1 C:HIS63 2.0 14.0 1.0
ND1 C:HIS71 2.0 15.3 1.0
CG C:ASP83 2.7 14.3 1.0
CE1 C:HIS80 2.8 14.9 1.0
CE1 C:HIS71 2.9 15.3 1.0
OD2 C:ASP83 2.9 14.2 1.0
CG C:HIS63 2.9 14.3 1.0
CE1 C:HIS63 3.0 13.7 1.0
CG C:HIS80 3.0 14.9 1.0
CG C:HIS71 3.2 15.7 1.0
CB C:HIS63 3.3 14.8 1.0
CB C:HIS80 3.5 15.2 1.0
CB C:HIS71 3.6 15.9 1.0
O C:LYS136 3.7 16.4 1.0
CA C:HIS71 3.8 16.1 1.0
NE2 C:HIS80 3.9 14.7 1.0
NE2 C:HIS63 4.1 13.8 1.0
CD2 C:HIS80 4.1 14.8 1.0
CD2 C:HIS63 4.1 13.9 1.0
NE2 C:HIS71 4.1 15.2 1.0
CB C:ASP83 4.2 14.2 1.0
CD2 C:HIS71 4.2 15.0 1.0
CA C:ASP83 4.7 14.5 1.0
N C:GLY72 4.7 16.3 1.0
O C:HOH357 4.7 26.3 1.0
N C:HIS80 4.8 15.4 1.0
C C:LYS136 4.8 17.3 1.0
N C:HIS71 4.8 16.4 1.0
CA C:HIS80 4.8 15.2 1.0
CA C:HIS63 4.8 14.9 1.0
C C:HIS71 4.8 16.2 1.0
N C:ASP83 5.0 14.4 1.0
CD2 C:HIS46 5.0 16.0 1.0

Zinc binding site 3 out of 6 in 6sph

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Zinc binding site 3 out of 6 in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group


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 Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:17.2
occ:1.00
 OD1 E:ASP83 1.9 15.4 1.0
ND1 E:HIS63 2.0 15.5 1.0
ND1 E:HIS80 2.0 18.0 1.0
ND1 E:HIS71 2.2 25.6 1.0
CG E:ASP83 2.7 15.4 1.0
OD2 E:ASP83 2.9 15.7 1.0
CE1 E:HIS80 2.9 17.7 1.0
CG E:HIS63 3.0 15.3 1.0
CE1 E:HIS63 3.0 15.5 1.0
CE1 E:HIS71 3.0 26.4 1.0
CG E:HIS80 3.1 18.0 1.0
CG E:HIS71 3.2 25.6 1.0
CB E:HIS63 3.2 15.1 1.0
CB E:HIS80 3.6 18.2 1.0
CB E:HIS71 3.6 25.2 1.0
O E:LYS136 3.8 21.3 1.0
CA E:HIS71 3.9 24.8 1.0
NE2 E:HIS80 4.0 17.7 1.0
CD2 E:HIS63 4.1 15.6 1.0
NE2 E:HIS63 4.1 15.9 1.0
CB E:ASP83 4.1 15.3 1.0
NE2 E:HIS71 4.2 26.8 1.0
CD2 E:HIS80 4.2 17.9 1.0
CD2 E:HIS71 4.3 25.9 1.0
CA E:ASP83 4.7 14.9 1.0
N E:GLY72 4.7 24.7 1.0
N E:HIS80 4.8 19.2 1.0
CA E:HIS63 4.8 14.8 1.0
C E:LYS136 4.8 21.8 1.0
CA E:HIS80 4.8 18.3 1.0
O E:HOH338 4.8 34.3 1.0
C E:HIS71 4.8 25.0 1.0
N E:HIS71 4.9 24.4 1.0
N E:ASP83 5.0 14.9 1.0
CD2 E:HIS46 5.0 15.0 1.0
O E:GLY72 5.0 23.4 1.0

Zinc binding site 4 out of 6 in 6sph

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Zinc binding site 4 out of 6 in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group


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 Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
G:Zn201

b:14.5
occ:1.00
 OD1 G:ASP83 2.0 16.3 1.0
ND1 G:HIS80 2.0 14.6 1.0
ND1 G:HIS63 2.0 15.3 1.0
ND1 G:HIS71 2.1 15.8 1.0
CG G:ASP83 2.8 15.4 1.0
CE1 G:HIS80 2.9 14.8 1.0
OD2 G:ASP83 3.0 14.9 1.0
CE1 G:HIS71 3.0 15.9 1.0
CE1 G:HIS63 3.0 14.9 1.0
CG G:HIS63 3.0 15.2 1.0
CG G:HIS80 3.1 14.2 1.0
CG G:HIS71 3.2 15.9 1.0
CB G:HIS63 3.3 15.4 1.0
CB G:HIS80 3.5 14.2 1.0
CB G:HIS71 3.5 16.0 1.0
O G:LYS136 3.7 20.6 1.0
CA G:HIS71 3.9 16.1 1.0
NE2 G:HIS80 4.0 14.5 1.0
NE2 G:HIS63 4.1 14.7 1.0
CD2 G:HIS80 4.1 14.5 1.0
CD2 G:HIS63 4.1 15.0 1.0
NE2 G:HIS71 4.1 16.0 1.0
CB G:ASP83 4.2 15.1 1.0
CD2 G:HIS71 4.2 15.8 1.0
CA G:ASP83 4.7 14.8 1.0
O G:HOH335 4.8 22.3 1.0
C G:LYS136 4.8 19.5 1.0
CA G:HIS80 4.8 14.6 1.0
N G:HIS80 4.8 14.8 1.0
N G:GLY72 4.8 15.7 1.0
CA G:HIS63 4.8 15.3 1.0
N G:HIS71 4.9 16.8 1.0
CD2 G:HIS46 4.9 15.9 1.0
C G:HIS71 4.9 15.6 1.0

Zinc binding site 5 out of 6 in 6sph

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Zinc binding site 5 out of 6 in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group


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 Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn302

b:16.8
occ:1.00
 OD1 J:ASP83 2.0 17.7 1.0
ND1 J:HIS80 2.0 17.1 1.0
ND1 J:HIS63 2.0 16.2 1.0
ND1 J:HIS71 2.0 18.7 1.0
CG J:ASP83 2.7 17.4 1.0
OD2 J:ASP83 2.8 16.7 1.0
CE1 J:HIS80 2.8 17.1 1.0
CE1 J:HIS71 2.9 18.9 1.0
CG J:HIS63 3.0 16.4 1.0
CE1 J:HIS63 3.0 15.9 1.0
CG J:HIS80 3.1 16.9 1.0
CG J:HIS71 3.2 18.6 1.0
CB J:HIS63 3.3 16.4 1.0
CB J:HIS80 3.6 17.2 1.0
CB J:HIS71 3.6 18.8 1.0
O J:LYS136 3.8 17.2 1.0
CA J:HIS71 3.9 19.1 1.0
NE2 J:HIS80 4.0 16.7 1.0
NE2 J:HIS71 4.1 18.9 1.0
CD2 J:HIS63 4.1 16.2 1.0
NE2 J:HIS63 4.1 16.0 1.0
CD2 J:HIS80 4.1 16.7 1.0
CB J:ASP83 4.2 17.6 1.0
CD2 J:HIS71 4.2 18.2 1.0
O J:HOH458 4.6 25.3 1.0
N J:HIS80 4.7 17.6 1.0
CA J:ASP83 4.7 17.6 1.0
CA J:HIS80 4.8 17.4 1.0
N J:GLY72 4.8 18.3 1.0
CA J:HIS63 4.8 16.4 1.0
C J:LYS136 4.8 18.8 1.0
CD2 J:HIS46 4.9 16.9 1.0
C J:HIS71 4.9 18.7 1.0
N J:HIS71 4.9 19.5 1.0

Zinc binding site 6 out of 6 in 6sph

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Zinc binding site 6 out of 6 in the A4V Mutant of Human Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group


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 Superoxide Dismutase 1 with Ebselen Bond in C2 Space Group within 5.0Å range:
probe atom residue distance (Å) B Occ
L:Zn201

b:15.1
occ:1.00
 ND1 L:HIS63 2.0 18.5 1.0
OD1 L:ASP83 2.0 12.6 1.0
ND1 L:HIS80 2.0 15.2 1.0
CD2 L:HIS71 2.1 18.6 1.0
CG L:ASP83 2.6 13.3 1.0
OD2 L:ASP83 2.7 13.5 1.0
CE1 L:HIS63 2.9 18.7 1.0
CE1 L:HIS80 2.9 15.2 1.0
CG L:HIS63 3.0 18.1 1.0
CG L:HIS80 3.0 15.3 1.0
NE2 L:HIS71 3.1 19.2 1.0
CG L:HIS71 3.2 18.6 1.0
CB L:HIS63 3.3 17.9 1.0
CB L:HIS80 3.4 15.6 1.0
O L:LYS136 3.6 18.6 1.0
CB L:HIS71 3.7 19.1 1.0
CA L:HIS71 4.0 19.1 1.0
NE2 L:HIS80 4.0 14.9 1.0
NE2 L:HIS63 4.0 18.2 1.0
CD2 L:HIS80 4.1 15.2 1.0
CD2 L:HIS63 4.1 18.2 1.0
CB L:ASP83 4.1 13.5 1.0
CE1 L:HIS71 4.3 19.0 1.0
ND1 L:HIS71 4.3 18.8 1.0
C L:LYS136 4.7 18.4 1.0
N L:HIS80 4.7 16.8 1.0
CA L:ASP83 4.7 13.5 1.0
CA L:HIS80 4.7 16.0 1.0
N L:GLY72 4.7 19.0 1.0
O L:HOH361 4.8 27.3 1.0
CA L:HIS63 4.9 17.6 1.0
C L:HIS71 4.9 19.1 1.0
O L:GLY72 4.9 17.8 1.0
CD2 L:HIS46 4.9 21.8 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: Tue Oct 29 07:33:15 2024

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