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Sodium 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
Chlorine (Cl) 9 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 6 in 6spk

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
E:Na208

b:21.9
occ:0.80
 O4 E:SO4206 2.8 37.5 0.5
O E:HOH340 3.0 32.5 1.0
CL E:CL213 3.1 36.2 0.7
O2 E:SO4206 3.2 37.1 0.5
S E:SO4206 3.6 36.6 0.5
O A:HOH340 3.7 33.7 1.0
CB E:ALA123 3.9 32.7 1.0
O E:HOH347 4.2 28.9 1.0
O E:HOH344 4.5 22.1 1.0
CD1 E:LEU42 4.5 30.0 1.0
O1 E:SO4206 4.5 38.2 0.5
O3 E:SO4206 4.6 34.9 0.5
NA E:NA209 4.8 28.0 0.8

Sodium binding site 2 out of 6 in 6spk

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
E:Na209

b:28.0
occ:0.80
 O E:HOH351 2.6 14.8 1.0
O3 E:SO4206 2.7 34.9 0.5
O E:HOH340 3.2 32.5 1.0
O4 E:SO4206 3.3 37.5 0.5
S E:SO4206 3.5 36.6 0.5
O E:HOH352 3.8 20.5 1.0
CG E:LEU42 4.0 30.1 1.0
CD1 E:LEU42 4.0 30.0 1.0
O2 E:SO4206 4.1 37.1 0.5
NA E:NA208 4.8 21.9 0.8
O1 E:SO4206 4.8 38.2 0.5
CD2 E:LEU42 4.8 30.6 1.0
NA E:NA210 5.0 20.0 0.8

Sodium binding site 3 out of 6 in 6spk

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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:Na210

b:20.0
occ:0.80
 OG1 E:THR88 2.9 31.9 1.0
O E:HOH351 3.2 14.8 1.0
CG2 E:THR88 3.3 33.8 1.0
CD2 E:LEU42 3.7 30.6 1.0
CB E:THR88 3.7 33.8 1.0
CG E:LEU42 4.6 30.1 1.0
NA E:NA209 5.0 28.0 0.8
CA E:THR88 5.0 33.4 1.0

Sodium binding site 4 out of 6 in 6spk

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
J:Na207

b:34.9
occ:0.80
 O J:HOH343 2.6 30.5 1.0
O J:HOH337 3.4 24.5 0.8
N J:LEU42 3.6 38.3 1.0
CA J:GLY41 3.9 41.4 1.0
C J:GLY41 4.2 40.6 1.0
CB J:LEU42 4.4 36.6 1.0
CA J:LEU42 4.5 35.8 1.0
CG J:LEU42 4.5 36.0 1.0
O J:LEU42 4.7 33.1 1.0
O J:GLU40 4.9 44.5 1.0

Sodium binding site 5 out of 6 in 6spk

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
J:Na208

b:26.0
occ:0.80
 CL J:CL210 2.8 36.9 0.8
O J:HOH337 4.0 24.5 0.8
CD1 J:LEU42 4.2 37.5 1.0
NA J:NA209 4.4 22.5 0.7
O J:HOH326 4.8 21.4 1.0

Sodium binding site 6 out of 6 in 6spk

Go back to Sodium Binding Sites List in 6spk
Sodium binding site 6 out of 6 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na 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
J:Na209

b:22.5
occ:0.70
 CL J:CL211 2.8 30.8 0.7
O J:HOH331 3.0 24.8 1.0
O J:HOH343 3.4 30.5 1.0
CB J:ALA123 3.7 36.6 1.0
CL J:CL210 4.0 36.9 0.8
CD1 J:LEU42 4.1 37.5 1.0
O J:HOH336 4.4 28.8 1.0
NA J:NA208 4.4 26.0 0.8
O J:HOH314 4.6 22.6 1.0
O J:ASP124 4.6 31.4 1.0
O J:HOH326 4.7 21.4 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 8 13:29:57 2024

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