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Chlorine 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
Zinc (Zn) 7 atoms
Sodium (Na) 6 atoms

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 9 binding sites of Chlorine where determined in the A4V Mutant of Human SOD1 with Ebselen Derivative 6, PDB code: 6spk:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Chlorine binding site 1 out of 9 in 6spk

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Chlorine binding site 1 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl210

b:31.9
occ:0.50
 O A:LYS136 3.0 43.8 1.0
O A:HOH331 3.0 30.8 1.0
N A:HIS63 3.2 35.8 1.0
CE A:LYS136 3.5 65.2 1.0
CB A:PRO62 3.5 37.0 1.0
CD A:LYS136 3.6 63.1 1.0
CG A:HIS63 3.6 37.2 1.0
CB A:HIS63 3.7 36.0 1.0
CE1 A:HIS80 3.8 35.7 1.0
NZ A:LYS136 3.8 64.4 1.0
ND1 A:HIS63 3.8 36.1 1.0
C A:LYS136 3.9 44.4 1.0
CG A:LYS136 3.9 59.3 1.0
CA A:PRO62 4.0 37.2 1.0
CA A:HIS63 4.0 36.1 1.0
C A:PRO62 4.1 37.4 1.0
CD2 A:HIS63 4.1 40.8 1.0
ND1 A:HIS80 4.2 35.7 1.0
CE1 A:HIS63 4.4 39.3 1.0
O A:HIS63 4.5 38.2 1.0
CA A:LYS136 4.6 45.9 1.0
NE2 A:HIS63 4.6 42.9 1.0
CG2 A:THR137 4.6 43.9 1.0
NE2 A:HIS80 4.6 36.4 1.0
N A:THR137 4.7 42.9 1.0
ZN A:ZN201 4.7 31.4 1.0
CA A:THR137 4.8 42.5 1.0
CB A:LYS136 4.8 52.0 1.0
C A:HIS63 4.8 36.5 1.0
CG A:PRO62 4.9 37.8 1.0

Chlorine binding site 2 out of 9 in 6spk

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Chlorine binding site 2 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl211

b:36.3
occ:0.60
 O A:HOH338 2.8 34.0 1.0
O A:ASP125 2.8 31.1 1.0
C A:ASP125 3.4 30.2 1.0
CA A:ASP125 3.6 29.9 1.0
CG A:LEU126 4.1 33.0 1.0
CB A:ASP125 4.3 29.9 1.0
O A:HOH337 4.3 17.0 1.0
CB A:LEU126 4.3 32.4 1.0
CD1 A:LEU126 4.3 32.0 1.0
N A:LEU126 4.4 31.2 1.0
O A:HOH330 4.4 25.3 1.0
O A:ASP124 4.5 32.6 1.0
CB A:LYS128 4.6 42.2 1.0
CD A:LYS128 4.6 51.2 1.0
CG A:LYS128 4.7 46.6 1.0
N A:ASP125 4.8 31.3 1.0
CA A:LEU126 4.9 32.3 1.0

Chlorine binding site 3 out of 9 in 6spk

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Chlorine binding site 3 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
A:Cl212

b:35.2
occ:0.70
 O A:HOH331 2.7 30.8 1.0
CE1 A:HIS120 3.4 36.1 1.0
CE1 A:HIS48 3.5 40.4 1.0
NH2 A:ARG143 3.6 40.7 1.0
CG2 A:THR137 3.8 43.9 1.0
NE A:ARG143 3.9 41.1 1.0
NE2 A:HIS63 4.0 42.9 1.0
CB A:THR137 4.1 43.9 1.0
NE2 A:HIS120 4.2 34.2 1.0
CZ A:ARG143 4.2 39.9 1.0
ND1 A:HIS120 4.2 34.5 1.0
NE2 A:HIS48 4.3 39.9 1.0
CD2 A:HIS63 4.4 40.8 1.0
ND1 A:HIS48 4.5 39.0 1.0
O A:GLY141 4.7 39.8 1.0
CA A:THR137 4.9 42.5 1.0
O3 A:SO4207 4.9 37.7 0.4
CE1 A:HIS63 5.0 39.3 1.0

Chlorine binding site 4 out of 9 in 6spk

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Chlorine binding site 4 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
E:Cl212

b:38.1
occ:0.70
 O E:HOH347 2.8 28.9 1.0
O E:HOH344 2.9 22.1 1.0
O E:HOH342 2.9 32.5 1.0
O E:ALA123 2.9 33.2 1.0
O E:ASN139 3.5 41.4 1.0
C E:ALA123 3.9 32.8 1.0
CB E:ALA123 4.2 32.7 1.0
CB E:ASN139 4.2 42.0 1.0
C E:ASN139 4.3 41.6 1.0
O E:GLY138 4.3 38.7 1.0
CB E:ASP125 4.4 26.3 1.0
O E:HOH317 4.4 27.5 1.0
CA E:ALA123 4.5 32.8 1.0
N E:ALA123 4.6 34.7 1.0
N E:ASP125 4.6 27.5 1.0
CB E:LYS122 4.6 43.2 1.0
O E:HOH348 4.6 37.7 1.0
CG E:LYS122 4.7 45.2 1.0
CD E:LYS122 4.8 45.1 1.0
CA E:ASN139 4.9 41.1 1.0
CA E:ASP125 4.9 27.0 1.0
C E:ASP124 4.9 29.3 1.0
N E:ASP124 4.9 31.6 1.0

Chlorine binding site 5 out of 9 in 6spk

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Chlorine binding site 5 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
E:Cl213

b:36.2
occ:0.70
 O E:HOH312 2.9 18.8 1.0
O E:HOH344 2.9 22.1 1.0
NA E:NA208 3.1 21.9 0.8
CB E:ALA123 3.8 32.7 1.0
O E:HOH340 3.9 32.5 1.0
CD1 E:LEU42 4.1 30.0 1.0
O E:ASP124 4.3 29.6 1.0
O E:HOH307 4.4 28.4 1.0
O E:HOH343 4.5 28.4 1.0
O E:HOH352 4.6 20.5 1.0
O4 E:SO4206 4.7 37.5 0.5
CA E:ASP125 4.8 27.0 1.0

Chlorine binding site 6 out of 9 in 6spk

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Chlorine binding site 6 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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
F:Cl209

b:32.8
occ:0.70
 O F:HOH333 2.8 14.4 1.0
O F:HOH331 3.0 24.8 1.0
O F:HOH308 5.0 25.7 1.0

Chlorine binding site 7 out of 9 in 6spk

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Chlorine binding site 7 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl 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:Cl210

b:36.9
occ:0.80
 NA J:NA208 2.8 26.0 0.8
NA J:NA209 4.0 22.5 0.7
O J:HOH321 4.3 24.8 1.0
O J:HOH336 4.5 28.8 1.0
O J:HOH334 4.9 30.1 1.0
O J:HOH314 4.9 22.6 1.0
CL J:CL211 4.9 30.8 0.7

Chlorine binding site 8 out of 9 in 6spk

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Chlorine binding site 8 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of A4V Mutant of Human SOD1 with Ebselen Derivative 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl211

b:30.8
occ:0.70
 O J:HOH326 2.7 21.4 1.0
O J:ASP124 2.7 31.4 1.0
NA J:NA209 2.8 22.5 0.7
O J:HOH314 3.0 22.6 1.0
C J:ASP124 3.8 30.9 1.0
CA J:ASP125 3.8 29.4 1.0
ND2 J:ASN86 3.8 31.8 1.0
O J:HOH331 3.9 24.8 1.0
CG J:LEU126 4.2 34.7 1.0
N J:ASP125 4.2 30.5 1.0
C J:ASP125 4.2 28.6 1.0
CD1 J:LEU42 4.3 37.5 1.0
O J:HOH336 4.5 28.8 1.0
CD1 J:LEU126 4.5 35.6 1.0
CB J:ALA123 4.5 36.6 1.0
O J:ASP125 4.6 26.9 1.0
N J:LEU126 4.8 28.8 1.0
CD2 J:LEU126 4.9 34.8 1.0
CB J:ASP125 4.9 29.1 1.0
CG J:ASN86 4.9 31.8 1.0
O J:HOH321 4.9 24.8 1.0
CL J:CL210 4.9 36.9 0.8

Chlorine binding site 9 out of 9 in 6spk

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Chlorine binding site 9 out of 9 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of A4V Mutant of Human SOD1 with Ebselen Derivative 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Cl212

b:29.2
occ:0.60
 O J:HOH340 2.7 31.3 1.0
N J:LYS75 3.4 47.5 1.0
CD J:PRO74 3.5 40.8 1.0
CA J:GLY73 3.5 35.8 1.0
CB J:LYS75 3.5 53.6 1.0
N J:PRO74 3.6 39.2 1.0
C J:GLY73 3.7 38.4 1.0
CG J:LYS75 4.0 61.2 1.0
CA J:LYS75 4.0 49.7 1.0
CG J:PRO74 4.0 40.9 1.0
CD J:LYS75 4.0 67.2 1.0
CD1 J:LEU126 4.2 35.6 1.0
C J:PRO74 4.4 44.4 1.0
O J:GLY73 4.4 41.5 1.0
N J:ASP76 4.5 49.2 1.0
CA J:PRO74 4.5 42.7 1.0
C J:LYS75 4.6 47.1 1.0
N J:GLY73 4.6 33.7 1.0
OD2 J:ASP76 4.9 52.1 1.0
CB J:PRO74 4.9 41.6 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: Mon Jul 29 15:06:18 2024

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