Fluorine 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:

Zinc (Zn) 7 atoms
Chlorine (Cl) 9 atoms
Sodium (Na) 6 atoms

Fluorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 18;

Binding sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 18 binding sites of Fluorine where determined in the A4V Mutant of Human SOD1 with Ebselen Derivative 6, PDB code: 6spk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 18 in 6spk

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Fluorine binding site 1 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F202

b:89.0
occ:0.75
F3 A:LQN202 0.0 89.0 0.8
C4 A:LQN202 1.3 87.5 0.8
F1 A:LQN202 2.2 87.5 0.8
F2 A:LQN202 2.2 87.5 0.8
C3 A:LQN202 2.3 86.2 0.8
C2 A:LQN202 3.1 88.5 0.8
C5 A:LQN202 3.1 84.0 0.8
C1 A:LQN202 4.3 86.5 0.8
C7 A:LQN202 4.3 83.2 0.8
F3 B:LQN202 4.7 79.1 0.8
C8 A:LQN202 4.8 85.6 0.8

Fluorine binding site 2 out of 18 in 6spk

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Fluorine binding site 2 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F202

b:87.5
occ:0.75
F1 A:LQN202 0.0 87.5 0.8
C4 A:LQN202 1.3 87.5 0.8
F2 A:LQN202 2.2 87.5 0.8
F3 A:LQN202 2.2 89.0 0.8
C3 A:LQN202 2.3 86.2 0.8
C5 A:LQN202 2.7 84.0 0.8
F3 B:LQN202 3.0 79.1 0.8
C2 B:LQN202 3.0 73.0 0.8
C3 B:LQN202 3.0 75.8 0.8
C1 B:LQN202 3.4 70.2 0.8
C4 B:LQN202 3.5 78.6 0.8
C5 B:LQN202 3.5 70.5 0.8
C2 A:LQN202 3.5 88.5 0.8
C8 B:LQN202 3.9 66.0 0.8
C7 B:LQN202 3.9 67.0 0.8
C7 A:LQN202 4.1 83.2 0.8
F2 B:LQN202 4.1 78.7 0.8
F1 B:LQN202 4.6 78.1 0.8
C1 A:LQN202 4.7 86.5 0.8
C8 A:LQN202 4.9 85.6 0.8
C9 B:LQN202 5.0 59.8 0.8

Fluorine binding site 3 out of 18 in 6spk

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Fluorine binding site 3 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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:F202

b:87.5
occ:0.75
F2 A:LQN202 0.0 87.5 0.8
C4 A:LQN202 1.3 87.5 0.8
F1 A:LQN202 2.2 87.5 0.8
F3 A:LQN202 2.2 89.0 0.8
C3 A:LQN202 2.3 86.2 0.8
C2 A:LQN202 2.7 88.5 0.8
C5 A:LQN202 3.5 84.0 0.8
C2 B:LQN202 3.9 73.0 0.8
C1 A:LQN202 4.1 86.5 0.8
C1 B:LQN202 4.1 70.2 0.8
C3 B:LQN202 4.6 75.8 0.8
F3 B:LQN202 4.6 79.1 0.8
C7 A:LQN202 4.7 83.2 0.8
C8 A:LQN202 4.9 85.6 0.8
C8 B:LQN202 4.9 66.0 0.8

Fluorine binding site 4 out of 18 in 6spk

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Fluorine binding site 4 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F202

b:79.1
occ:0.75
F3 B:LQN202 0.0 79.1 0.8
C4 B:LQN202 1.3 78.6 0.8
F2 B:LQN202 2.2 78.7 0.8
F1 B:LQN202 2.2 78.1 0.8
C3 B:LQN202 2.3 75.8 0.8
F1 A:LQN202 3.0 87.5 0.8
C5 B:LQN202 3.2 70.5 0.8
C2 B:LQN202 3.2 73.0 0.8
C4 A:LQN202 4.2 87.5 0.8
C7 B:LQN202 4.4 67.0 0.8
C1 B:LQN202 4.4 70.2 0.8
F2 A:LQN202 4.6 87.5 0.8
F3 A:LQN202 4.7 89.0 0.8
C8 B:LQN202 4.9 66.0 0.8

Fluorine binding site 5 out of 18 in 6spk

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Fluorine binding site 5 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F202

b:78.1
occ:0.75
F1 B:LQN202 0.0 78.1 0.8
C4 B:LQN202 1.3 78.6 0.8
F2 B:LQN202 2.2 78.7 0.8
F3 B:LQN202 2.2 79.1 0.8
C3 B:LQN202 2.3 75.8 0.8
C5 B:LQN202 2.7 70.5 0.8
C2 B:LQN202 3.5 73.0 0.8
C7 B:LQN202 4.1 67.0 0.8
C1 B:LQN202 4.6 70.2 0.8
F1 A:LQN202 4.6 87.5 0.8
C8 B:LQN202 4.9 66.0 0.8

Fluorine binding site 6 out of 18 in 6spk

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Fluorine binding site 6 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
B:F202

b:78.7
occ:0.75
F2 B:LQN202 0.0 78.7 0.8
C4 B:LQN202 1.3 78.6 0.8
F3 B:LQN202 2.2 79.1 0.8
F1 B:LQN202 2.2 78.1 0.8
C3 B:LQN202 2.3 75.8 0.8
C2 B:LQN202 2.6 73.0 0.8
C5 B:LQN202 3.6 70.5 0.8
OD2 B:ASP109 3.9 80.4 1.0
C1 B:LQN202 4.0 70.2 0.8
F1 A:LQN202 4.1 87.5 0.8
OD1 B:ASP109 4.2 81.4 1.0
CG B:ASP109 4.5 74.5 1.0
C7 B:LQN202 4.7 67.0 0.8
C8 B:LQN202 4.9 66.0 0.8

Fluorine binding site 7 out of 18 in 6spk

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Fluorine binding site 7 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
E:F202

b:0.1
occ:0.60
F3 E:LQN202 0.0 0.1 0.6
C4 E:LQN202 1.3 0.2 0.6
F2 E:LQN202 2.1 0.3 0.6
F1 E:LQN202 2.2 1.0 0.6
C3 E:LQN202 2.3 99.5 0.6
C5 E:LQN202 2.7 98.6 0.6
CB J:ALA1 3.1 96.4 1.0
C2 E:LQN202 3.5 97.9 0.6
C7 E:LQN202 4.1 99.6 0.6
O J:LYS23 4.3 81.8 1.0
CA J:ALA1 4.5 93.7 1.0
CG2 J:THR2 4.6 80.6 1.0
N J:THR2 4.7 79.9 1.0
C1 E:LQN202 4.7 97.2 0.6
C8 E:LQN202 4.9 98.1 0.6
N J:ALA1 4.9 93.6 1.0
OD1 E:ASP109 5.0 0.0 1.0
C J:ALA1 5.0 86.8 1.0
CB J:THR2 5.0 77.0 1.0

Fluorine binding site 8 out of 18 in 6spk

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Fluorine binding site 8 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
E:F202

b:1.0
occ:0.60
F1 E:LQN202 0.0 1.0 0.6
C4 E:LQN202 1.3 0.2 0.6
F2 E:LQN202 2.2 0.3 0.6
F3 E:LQN202 2.2 0.1 0.6
C3 E:LQN202 2.3 99.5 0.6
C2 E:LQN202 2.7 97.9 0.6
CG2 J:THR2 3.2 80.6 1.0
C5 E:LQN202 3.6 98.6 0.6
C1 E:LQN202 4.1 97.2 0.6
CB J:THR2 4.1 77.0 1.0
N J:SER25 4.2 83.0 1.0
O J:GLN22 4.4 81.8 1.0
CB J:ALA1 4.4 96.4 1.0
OG J:SER107 4.5 71.6 1.0
O J:LYS23 4.6 81.8 1.0
N J:THR2 4.6 79.9 1.0
C J:GLU24 4.6 82.9 1.0
OD1 E:ASP109 4.7 0.0 1.0
C7 E:LQN202 4.7 99.6 0.6
CA J:SER25 4.7 82.9 1.0
C8 E:LQN202 4.9 98.1 0.6
CB J:SER25 4.9 82.6 1.0

Fluorine binding site 9 out of 18 in 6spk

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Fluorine binding site 9 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F 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
E:F202

b:0.3
occ:0.60
F2 E:LQN202 0.0 0.3 0.6
C4 E:LQN202 1.3 0.2 0.6
F3 E:LQN202 2.1 0.1 0.6
F1 E:LQN202 2.2 1.0 0.6
C3 E:LQN202 2.3 99.5 0.6
C5 E:LQN202 3.1 98.6 0.6
C2 E:LQN202 3.2 97.9 0.6
N J:SER25 3.3 83.0 1.0
OD1 E:ASP109 3.4 0.0 1.0
OD2 E:ASP109 3.5 90.7 1.0
CG E:ASP109 3.7 90.3 1.0
O J:LYS23 3.8 81.8 1.0
C J:GLU24 3.9 82.9 1.0
CA J:GLU24 4.0 81.9 1.0
CA J:SER25 4.2 82.9 1.0
CB J:SER25 4.2 82.6 1.0
C7 E:LQN202 4.4 99.6 0.6
C1 E:LQN202 4.4 97.2 0.6
C J:LYS23 4.5 78.1 1.0
N J:GLU24 4.6 78.8 1.0
CB J:ALA1 4.7 96.4 1.0
CB E:ASP109 4.8 82.6 1.0
O J:GLU24 4.9 90.0 1.0
C8 E:LQN202 4.9 98.1 0.6
OE1 J:GLU24 4.9 80.2 0.6

Fluorine binding site 10 out of 18 in 6spk

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Fluorine binding site 10 out of 18 in the A4V Mutant of Human SOD1 with Ebselen Derivative 6


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of A4V Mutant of Human SOD1 with Ebselen Derivative 6 within 5.0Å range:
probe atom residue distance (Å) B Occ
F:F202

b:0.7
occ:0.50
F3 F:LQN202 0.0 0.7 0.5
C4 F:LQN202 1.3 0.5 0.5
F2 F:LQN202 2.2 0.2 0.5
F1 F:LQN202 2.2 0.3 0.5
C3 F:LQN202 2.3 0.5 0.5
C2 F:LQN202 2.8 0.1 0.5
C5 F:LQN202 3.4 0.0 0.5
C1 F:LQN202 4.2 0.0 0.5
C7 F:LQN202 4.6 0.1 0.5
C8 F:LQN202 4.9 0.5 0.5

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: Sun Dec 13 13:12:26 2020

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