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

Enzymatic activity of A4V Mutant of Human SOD1 with Ebselen Derivative 6

All present enzymatic activity of A4V Mutant of Human SOD1 with Ebselen Derivative 6:
1.15.1.1;

Protein crystallography data

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

Resolution Low / High (Å) 97.08 / 2.77
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 112.663, 195.546, 76.340, 90.00, 98.08, 90.00
R / Rfree (%) 21.1 / 22.9

Other elements in 6spk:

The structure of A4V Mutant of Human SOD1 with Ebselen Derivative 6 also contains other interesting chemical elements:

Fluorine (F) 18 atoms
Chlorine (Cl) 9 atoms
Sodium (Na) 6 atoms

Zinc Binding Sites:

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

Zinc binding site 1 out of 7 in 6spk

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Zinc binding site 1 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:31.4
occ:1.00
 ND1 A:HIS63 1.9 36.1 1.0
OD1 A:ASP83 2.0 29.5 1.0
ND1 A:HIS71 2.1 37.1 1.0
ND1 A:HIS80 2.1 35.7 1.0
CG A:ASP83 2.7 28.8 1.0
OD2 A:ASP83 2.7 29.7 1.0
CE1 A:HIS80 2.9 35.7 1.0
CG A:HIS63 2.9 37.2 1.0
CE1 A:HIS63 2.9 39.3 1.0
CE1 A:HIS71 2.9 39.4 1.0
CG A:HIS80 3.1 36.4 1.0
CG A:HIS71 3.1 38.2 1.0
CB A:HIS63 3.3 36.0 1.0
CB A:HIS71 3.5 37.6 1.0
CB A:HIS80 3.6 36.4 1.0
O A:LYS136 3.7 43.8 1.0
CA A:HIS71 3.9 38.5 1.0
NE2 A:HIS80 4.0 36.4 1.0
NE2 A:HIS63 4.0 42.9 1.0
CD2 A:HIS63 4.0 40.8 1.0
CB A:ASP83 4.1 28.6 1.0
NE2 A:HIS71 4.1 39.5 1.0
CD2 A:HIS80 4.1 37.1 1.0
CD2 A:HIS71 4.2 39.8 1.0
CL A:CL210 4.7 31.9 0.5
CA A:ASP83 4.7 29.0 1.0
C A:LYS136 4.8 44.4 1.0
N A:HIS80 4.8 37.4 1.0
CA A:HIS63 4.8 36.1 1.0
CA A:HIS80 4.8 36.0 1.0
N A:GLY72 4.8 37.4 1.0
C A:HIS71 4.9 37.9 1.0
N A:HIS71 4.9 40.2 1.0
CD2 A:HIS46 5.0 34.1 1.0
N A:ASP83 5.0 29.7 1.0

Zinc binding site 2 out of 7 in 6spk

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Zinc binding site 2 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:29.8
occ:1.00
 OD1 B:ASP83 2.0 29.1 1.0
ND1 B:HIS63 2.0 30.9 1.0
ND1 B:HIS71 2.0 38.7 1.0
ND1 B:HIS80 2.1 37.9 1.0
CG B:ASP83 2.6 29.5 1.0
OD2 B:ASP83 2.7 30.9 1.0
CE1 B:HIS80 2.9 38.0 1.0
CE1 B:HIS71 2.9 39.7 1.0
CE1 B:HIS63 3.0 32.3 1.0
CG B:HIS63 3.0 31.2 1.0
CG B:HIS71 3.1 37.4 1.0
CG B:HIS80 3.1 38.8 1.0
CB B:HIS63 3.3 31.2 1.0
CB B:HIS71 3.5 37.2 1.0
CB B:HIS80 3.6 39.3 1.0
O B:LYS136 3.7 40.8 1.0
CA B:HIS71 3.9 36.6 1.0
NE2 B:HIS80 4.0 38.1 1.0
CB B:ASP83 4.1 29.7 1.0
NE2 B:HIS71 4.1 39.5 1.0
NE2 B:HIS63 4.1 32.2 1.0
CD2 B:HIS63 4.1 31.1 1.0
CD2 B:HIS80 4.1 39.2 1.0
CD2 B:HIS71 4.2 38.7 1.0
CA B:ASP83 4.7 29.9 1.0
N B:HIS80 4.7 42.8 1.0
C B:LYS136 4.8 40.4 1.0
N B:GLY72 4.8 33.9 1.0
CA B:HIS80 4.8 40.5 1.0
CA B:HIS63 4.8 32.2 1.0
C B:HIS71 4.9 36.2 1.0
ND1 B:HIS46 4.9 33.4 1.0
O B:HOH315 4.9 35.1 1.0
N B:HIS71 4.9 37.7 1.0
N B:ASP83 5.0 30.4 1.0

Zinc binding site 3 out of 7 in 6spk

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Zinc binding site 3 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:31.6
occ:1.00
 OD1 E:ASP83 2.0 28.0 1.0
ND1 E:HIS80 2.0 31.1 1.0
ND1 E:HIS71 2.0 34.4 1.0
ND1 E:HIS63 2.1 33.9 1.0
CG E:ASP83 2.6 27.9 1.0
OD2 E:ASP83 2.6 27.4 1.0
CE1 E:HIS80 2.9 31.0 1.0
CE1 E:HIS71 2.9 36.0 1.0
CG E:HIS63 3.0 33.5 1.0
CE1 E:HIS63 3.0 34.9 1.0
CG E:HIS80 3.1 31.5 1.0
CG E:HIS71 3.1 34.8 1.0
CB E:HIS63 3.3 32.6 1.0
CB E:HIS71 3.5 35.5 1.0
CB E:HIS80 3.5 32.8 1.0
O E:LYS136 3.7 40.7 1.0
CA E:HIS71 3.8 35.9 1.0
NE2 E:HIS80 4.0 30.8 1.0
CB E:ASP83 4.0 27.8 1.0
CD2 E:HIS80 4.1 31.7 1.0
NE2 E:HIS71 4.1 36.5 1.0
NE2 E:HIS63 4.2 35.8 1.0
CD2 E:HIS63 4.2 36.0 1.0
CD2 E:HIS71 4.2 35.0 1.0
O E:HOH322 4.6 20.3 1.0
CA E:ASP83 4.7 29.2 1.0
N E:HIS80 4.7 33.5 1.0
N E:GLY72 4.7 33.7 1.0
CA E:HIS80 4.7 33.0 1.0
C E:LYS136 4.8 40.7 1.0
C E:HIS71 4.8 34.9 1.0
N E:HIS71 4.9 35.9 1.0
CA E:HIS63 4.9 33.0 1.0
N E:ASP83 5.0 29.8 1.0

Zinc binding site 4 out of 7 in 6spk

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Zinc binding site 4 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn201

b:46.9
occ:1.00
 OD1 F:ASP83 1.9 53.0 1.0
ND1 F:HIS63 1.9 39.1 1.0
ND1 F:HIS71 2.1 54.3 1.0
ND1 F:HIS80 2.1 52.4 1.0
CG F:ASP83 2.6 47.9 1.0
OD2 F:ASP83 2.7 47.3 1.0
CE1 F:HIS71 2.9 55.5 1.0
CE1 F:HIS63 2.9 38.8 1.0
CG F:HIS63 2.9 39.6 1.0
CE1 F:HIS80 2.9 49.4 1.0
CG F:HIS80 3.1 52.2 1.0
CG F:HIS71 3.2 54.1 1.0
CB F:HIS63 3.3 41.8 1.0
CB F:HIS71 3.6 53.8 1.0
CB F:HIS80 3.6 51.4 1.0
O F:LYS136 3.8 54.0 1.0
CA F:HIS71 4.0 54.1 1.0
NE2 F:HIS63 4.0 39.3 1.0
CD2 F:HIS63 4.0 39.3 1.0
CB F:ASP83 4.1 48.5 1.0
NE2 F:HIS80 4.1 51.5 1.0
NE2 F:HIS71 4.1 53.5 1.0
CD2 F:HIS80 4.2 51.5 1.0
CD2 F:HIS71 4.2 52.8 1.0
CA F:ASP83 4.6 48.0 1.0
N F:HIS80 4.8 57.8 1.0
CA F:HIS80 4.8 53.7 1.0
N F:GLY72 4.8 52.9 1.0
CA F:HIS63 4.8 46.4 1.0
C F:LYS136 4.8 59.7 1.0
CD2 F:HIS46 4.9 41.2 1.0
C F:HIS71 4.9 53.3 1.0
N F:ASP83 4.9 47.1 1.0
N F:HIS71 5.0 56.8 1.0

Zinc binding site 5 out of 7 in 6spk

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Zinc binding site 5 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:26.2
occ:0.70
 ND1 I:HIS63 2.0 59.0 1.0
ND1 I:HIS80 2.0 56.2 1.0
OD1 I:ASP83 2.1 37.3 1.0
ND1 I:HIS71 2.1 60.2 1.0
CG I:ASP83 2.7 37.3 1.0
OD2 I:ASP83 2.7 35.5 1.0
CE1 I:HIS80 2.8 54.0 1.0
CG I:HIS63 2.9 57.5 1.0
CE1 I:HIS63 3.0 60.3 1.0
CE1 I:HIS71 3.0 60.5 1.0
CG I:HIS80 3.1 53.4 1.0
CG I:HIS71 3.1 58.3 1.0
CB I:HIS63 3.3 57.9 1.0
CB I:HIS71 3.5 58.6 1.0
CB I:HIS80 3.6 50.9 1.0
O I:LYS136 3.6 55.3 1.0
CA I:HIS71 3.9 55.8 1.0
NE2 I:HIS80 3.9 55.4 1.0
CD2 I:HIS63 4.1 57.9 1.0
NE2 I:HIS63 4.1 57.2 1.0
CD2 I:HIS80 4.1 53.6 1.0
NE2 I:HIS71 4.1 56.4 1.0
CB I:ASP83 4.2 41.4 1.0
CD2 I:HIS71 4.2 57.0 1.0
C I:LYS136 4.7 57.6 1.0
N I:HIS80 4.7 58.3 1.0
N I:GLY72 4.8 50.9 1.0
CA I:HIS80 4.8 52.5 1.0
CA I:HIS63 4.8 61.2 1.0
CA I:ASP83 4.8 43.3 1.0
N I:HIS71 4.9 55.4 1.0
C I:HIS71 4.9 53.2 1.0
O I:HOH314 4.9 27.9 0.8

Zinc binding site 6 out of 7 in 6spk

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Zinc binding site 6 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn202

b:23.7
occ:0.15
 NE2 I:HIS120 1.9 44.3 1.0
NE2 I:HIS48 2.0 49.6 1.0
ND1 I:HIS46 2.2 50.6 1.0
NE2 I:HIS63 2.5 57.2 1.0
CE1 I:HIS120 2.7 45.9 1.0
CE1 I:HIS48 2.8 49.0 1.0
CD2 I:HIS120 2.9 46.9 1.0
CD2 I:HIS63 2.9 57.9 1.0
CG I:HIS46 3.0 48.1 1.0
CD2 I:HIS48 3.1 49.4 1.0
CB I:HIS46 3.2 45.5 1.0
CE1 I:HIS46 3.2 52.3 1.0
O2 I:SO4205 3.4 42.9 0.5
CE1 I:HIS63 3.7 60.3 1.0
ND1 I:HIS120 3.8 48.7 1.0
CG I:HIS120 3.9 47.8 1.0
ND1 I:HIS48 3.9 46.0 1.0
CG I:HIS63 4.1 57.5 1.0
CG I:HIS48 4.1 48.0 1.0
CD2 I:HIS46 4.1 48.9 1.0
NE2 I:HIS46 4.2 49.6 1.0
O I:HOH320 4.3 24.2 0.8
O4 I:SO4205 4.4 43.0 0.5
CA I:HIS46 4.4 43.6 1.0
S I:SO4205 4.5 43.6 0.5
ND1 I:HIS63 4.5 59.0 1.0
CB I:VAL118 4.5 38.0 1.0
N I:HIS46 4.7 42.1 1.0
CG1 I:VAL118 4.7 37.3 1.0

Zinc binding site 7 out of 7 in 6spk

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Zinc binding site 7 out of 7 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


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 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn202

b:36.2
occ:1.00
 OD1 J:ASP83 1.9 35.6 1.0
ND1 J:HIS80 2.0 37.8 1.0
ND1 J:HIS71 2.1 49.0 1.0
ND1 J:HIS63 2.1 34.3 1.0
CG J:ASP83 2.5 34.5 1.0
OD2 J:ASP83 2.6 32.9 1.0
CE1 J:HIS80 2.9 37.6 1.0
CE1 J:HIS71 3.0 49.2 1.0
CG J:HIS63 3.0 35.7 1.0
CG J:HIS80 3.0 37.9 1.0
CE1 J:HIS63 3.1 36.4 1.0
CG J:HIS71 3.1 45.0 1.0
CB J:HIS63 3.3 36.4 1.0
CB J:HIS80 3.5 40.4 1.0
CB J:HIS71 3.5 43.1 1.0
O J:LYS136 3.8 38.0 1.0
CA J:HIS71 3.9 41.3 1.0
NE2 J:HIS80 4.0 36.8 1.0
CB J:ASP83 4.0 35.3 1.0
CD2 J:HIS80 4.1 37.5 1.0
NE2 J:HIS71 4.1 48.1 1.0
CD2 J:HIS63 4.2 36.9 1.0
NE2 J:HIS63 4.2 36.0 1.0
CD2 J:HIS71 4.2 46.8 1.0
O J:HOH316 4.5 28.0 0.8
CA J:ASP83 4.6 35.8 1.0
N J:HIS80 4.6 43.1 1.0
CA J:HIS80 4.7 43.2 1.0
N J:GLY72 4.7 34.6 1.0
C J:LYS136 4.8 38.6 1.0
C J:HIS71 4.8 38.0 1.0
CA J:HIS63 4.9 37.9 1.0
N J:HIS71 4.9 43.3 1.0
N J:ASP83 4.9 36.3 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 07:33:50 2024

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