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Zinc in PDB 6a9o: Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis

Enzymatic activity of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis

All present enzymatic activity of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis:
1.15.1.1;

Protein crystallography data

The structure of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis, PDB code: 6a9o was solved by R.Manjula, B.Padmanabhan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 20.00 / 2.50
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 164.367, 203.692, 144.211, 90.00, 90.00, 90.00
R / Rfree (%) 16.3 / 23.7

Zinc Binding Sites:

The binding sites of Zinc atom in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis (pdb code 6a9o). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis, PDB code: 6a9o:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 6a9o

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Zinc binding site 1 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn201

b:49.5
occ:1.00
 ND1 A:HIS80 2.1 34.9 1.0
ND1 A:HIS63 2.1 42.0 1.0
OD1 A:ASP83 2.2 35.1 1.0
ND1 A:HIS71 2.2 39.3 1.0
CG A:ASP83 2.9 36.9 1.0
CE1 A:HIS80 3.0 33.6 1.0
OD2 A:ASP83 3.0 36.9 1.0
CG A:HIS80 3.0 38.9 1.0
CE1 A:HIS63 3.1 45.2 1.0
CE1 A:HIS71 3.1 37.0 1.0
CG A:HIS63 3.1 41.8 1.0
CG A:HIS71 3.3 35.5 1.0
CB A:HIS80 3.4 38.0 1.0
CB A:HIS63 3.4 32.9 1.0
CB A:HIS71 3.6 36.2 1.0
CA A:HIS71 3.9 37.2 1.0
O A:LYS136 4.1 46.6 1.0
NE2 A:HIS80 4.1 37.8 1.0
CD2 A:HIS80 4.1 40.3 1.0
NE2 A:HIS63 4.2 44.0 1.0
CD2 A:HIS63 4.3 46.4 1.0
NE2 A:HIS71 4.3 38.0 1.0
CB A:ASP83 4.4 35.1 1.0
CD2 A:HIS71 4.4 37.3 1.0
CA A:HIS80 4.8 34.5 1.0
CA A:ASP83 4.8 34.7 1.0
N A:GLY72 4.8 37.0 1.0
N A:HIS80 4.8 39.0 1.0
O A:HOH325 4.8 40.2 1.0
N A:HIS71 4.8 38.9 1.0
C A:HIS71 4.9 38.7 1.0
N A:ASP83 4.9 34.9 1.0
CA A:HIS63 5.0 34.4 1.0
C A:LYS136 5.0 41.4 1.0

Zinc binding site 2 out of 9 in 6a9o

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Zinc binding site 2 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn201

b:39.6
occ:1.00
 ND1 B:HIS63 2.0 30.6 1.0
ND1 B:HIS80 2.0 30.3 1.0
OD1 B:ASP83 2.0 25.9 1.0
ND1 B:HIS71 2.2 28.4 1.0
CG B:ASP83 2.9 27.5 1.0
CE1 B:HIS80 2.9 28.4 1.0
CE1 B:HIS63 2.9 29.0 1.0
CE1 B:HIS71 3.0 27.1 1.0
OD2 B:ASP83 3.0 30.4 1.0
CG B:HIS63 3.1 31.2 1.0
CG B:HIS80 3.1 30.5 1.0
CG B:HIS71 3.2 28.7 1.0
CB B:HIS63 3.5 29.0 1.0
CB B:HIS80 3.5 28.8 1.0
CB B:HIS71 3.6 25.6 1.0
O B:LYS136 3.9 35.7 1.0
CA B:HIS71 4.0 29.5 1.0
NE2 B:HIS80 4.0 31.8 1.0
NE2 B:HIS63 4.1 30.5 1.0
CD2 B:HIS80 4.1 29.9 1.0
CD2 B:HIS63 4.2 29.8 1.0
NE2 B:HIS71 4.2 27.6 1.0
CD2 B:HIS71 4.3 27.6 1.0
CB B:ASP83 4.3 28.5 1.0
N B:HIS80 4.7 30.6 1.0
O B:HOH325 4.7 30.6 1.0
CA B:HIS80 4.8 26.8 1.0
N B:GLY72 4.8 26.7 1.0
CA B:ASP83 4.8 28.6 1.0
C B:LYS136 4.8 35.8 1.0
N B:HIS71 4.9 31.2 1.0
CD2 B:HIS46 4.9 28.4 1.0
N B:ASP83 4.9 29.6 1.0
C B:HIS71 4.9 28.8 1.0
CA B:HIS63 5.0 30.8 1.0

Zinc binding site 3 out of 9 in 6a9o

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Zinc binding site 3 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn201

b:49.2
occ:1.00
 ND1 C:HIS80 2.1 44.5 1.0
OD1 C:ASP83 2.1 40.1 1.0
ND1 C:HIS71 2.3 42.7 1.0
ND1 C:HIS63 2.4 46.1 1.0
CG C:ASP83 2.8 39.9 1.0
OD2 C:ASP83 2.8 37.6 1.0
CG C:HIS80 3.0 45.5 1.0
CE1 C:HIS80 3.0 43.6 1.0
CG C:HIS71 3.2 41.5 1.0
CE1 C:HIS71 3.3 42.0 1.0
CB C:HIS80 3.3 39.7 1.0
CG C:HIS63 3.3 40.8 1.0
CE1 C:HIS63 3.4 48.6 1.0
CB C:HIS71 3.5 41.1 1.0
CB C:HIS63 3.5 42.6 1.0
CA C:HIS71 3.8 40.7 1.0
O C:LYS136 3.8 54.2 1.0
CD2 C:HIS80 4.1 51.1 1.0
NE2 C:HIS80 4.1 54.8 1.0
CB C:ASP83 4.2 34.9 1.0
NE2 C:HIS71 4.4 44.3 1.0
CD2 C:HIS71 4.4 44.4 1.0
CD2 C:HIS63 4.5 46.4 1.0
NE2 C:HIS63 4.5 48.2 1.0
CA C:HIS80 4.5 39.6 1.0
N C:HIS80 4.6 46.9 1.0
CA C:ASP83 4.8 32.4 1.0
N C:GLY72 4.8 43.9 1.0
C C:LYS136 4.8 50.9 1.0
N C:HIS71 4.8 43.0 1.0
C C:HIS71 4.8 43.2 1.0
N C:ASP83 4.9 37.7 1.0

Zinc binding site 4 out of 9 in 6a9o

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Zinc binding site 4 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Zn201

b:41.1
occ:1.00
 OD1 D:ASP83 1.9 33.1 1.0
ND1 D:HIS63 2.2 31.5 1.0
ND1 D:HIS80 2.2 30.9 1.0
ND1 D:HIS71 2.2 31.8 1.0
CG D:ASP83 2.7 30.1 1.0
OD2 D:ASP83 2.9 31.6 1.0
CE1 D:HIS80 3.0 27.8 1.0
CE1 D:HIS71 3.0 29.0 1.0
CE1 D:HIS63 3.1 27.4 1.0
CG D:HIS63 3.2 33.8 1.0
CG D:HIS80 3.2 30.0 1.0
CG D:HIS71 3.2 30.1 1.0
CB D:HIS63 3.5 31.3 1.0
CB D:HIS80 3.6 30.1 1.0
CB D:HIS71 3.6 28.4 1.0
O D:LYS136 3.9 32.6 1.0
CA D:HIS71 4.0 30.6 1.0
NE2 D:HIS80 4.1 31.9 1.0
CB D:ASP83 4.2 30.8 1.0
NE2 D:HIS71 4.2 31.5 1.0
CD2 D:HIS80 4.2 32.6 1.0
NE2 D:HIS63 4.2 30.6 1.0
CD2 D:HIS63 4.3 36.0 1.0
CD2 D:HIS71 4.3 27.1 1.0
CA D:ASP83 4.6 27.2 1.0
N D:HIS80 4.8 30.1 1.0
CA D:HIS80 4.8 31.0 1.0
N D:GLY72 4.8 27.4 1.0
N D:ASP83 4.9 27.3 1.0
C D:LYS136 4.9 33.7 1.0
C D:HIS71 5.0 29.4 1.0
N D:HIS71 5.0 32.4 1.0

Zinc binding site 5 out of 9 in 6a9o

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Zinc binding site 5 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Zn201

b:62.8
occ:1.00
 ND1 E:HIS80 2.2 52.5 1.0
ND1 E:HIS63 2.3 43.2 1.0
OD1 E:ASP83 2.4 46.7 1.0
ND1 E:HIS71 2.5 60.5 1.0
OD2 E:ASP83 2.9 55.3 1.0
CG E:ASP83 3.0 53.6 1.0
CE1 E:HIS80 3.1 50.8 1.0
CG E:HIS63 3.1 42.5 1.0
CG E:HIS80 3.2 59.0 1.0
CE1 E:HIS63 3.3 50.5 1.0
CB E:HIS63 3.3 36.7 1.0
CE1 E:HIS71 3.4 65.0 1.0
CB E:HIS80 3.5 45.4 1.0
CG E:HIS71 3.6 67.8 1.0
CB E:HIS71 3.9 61.8 1.0
CA E:HIS71 4.1 62.3 1.0
O E:LYS136 4.2 61.5 1.0
NE2 E:HIS80 4.2 62.9 1.0
CD2 E:HIS63 4.3 49.4 1.0
CD2 E:HIS80 4.3 62.0 1.0
NE2 E:HIS63 4.3 54.3 1.0
CB E:ASP83 4.5 41.4 1.0
CD2 E:HIS46 4.5 45.9 1.0
NE2 E:HIS71 4.5 68.6 1.0
N E:HIS80 4.6 44.4 1.0
CD2 E:HIS71 4.6 74.0 1.0
CA E:HIS80 4.7 43.1 1.0
CA E:HIS63 4.8 37.8 1.0
C E:LYS136 5.0 64.7 1.0
N E:GLY72 5.0 56.3 1.0

Zinc binding site 6 out of 9 in 6a9o

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Zinc binding site 6 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Zn202

b:39.5
occ:1.00
 OD1 F:ASP83 2.0 31.2 1.0
ND1 F:HIS63 2.1 33.2 1.0
ND1 F:HIS80 2.1 31.1 1.0
ND1 F:HIS71 2.2 25.3 1.0
CG F:ASP83 2.8 33.9 1.0
CE1 F:HIS80 3.0 28.8 1.0
OD2 F:ASP83 3.0 39.2 1.0
CE1 F:HIS63 3.0 31.6 1.0
CE1 F:HIS71 3.0 26.9 1.0
CG F:HIS80 3.1 28.2 1.0
CG F:HIS63 3.1 33.4 1.0
CG F:HIS71 3.3 26.1 1.0
CB F:HIS80 3.5 25.9 1.0
CB F:HIS63 3.5 32.8 1.0
CB F:HIS71 3.8 27.3 1.0
O F:LYS136 4.0 32.4 1.0
NE2 F:HIS80 4.1 29.7 1.0
CA F:HIS71 4.1 29.3 1.0
CD2 F:HIS80 4.1 29.6 1.0
NE2 F:HIS63 4.1 31.1 1.0
NE2 F:HIS71 4.2 28.3 1.0
CB F:ASP83 4.2 30.6 1.0
CD2 F:HIS63 4.2 32.2 1.0
CD2 F:HIS71 4.4 24.2 1.0
CA F:ASP83 4.6 28.4 1.0
N F:HIS80 4.8 31.9 1.0
CA F:HIS80 4.8 28.5 1.0
N F:ASP83 4.8 28.3 1.0
O F:HOH383 4.8 34.6 1.0
CD2 F:HIS46 4.9 25.4 1.0
N F:GLY72 4.9 26.3 1.0
C F:LYS136 5.0 32.8 1.0
CA F:HIS63 5.0 33.1 1.0

Zinc binding site 7 out of 9 in 6a9o

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Zinc binding site 7 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Zn201

b:48.3
occ:1.00
 OD1 H:ASP83 2.0 36.3 1.0
ND1 H:HIS80 2.1 45.3 1.0
ND1 H:HIS71 2.1 35.5 1.0
ND1 H:HIS63 2.2 37.0 1.0
CG H:ASP83 2.7 39.3 1.0
OD2 H:ASP83 2.9 42.6 1.0
CE1 H:HIS80 2.9 37.5 1.0
CE1 H:HIS71 3.0 39.5 1.0
CG H:HIS80 3.0 44.2 1.0
CG H:HIS63 3.1 38.0 1.0
CG H:HIS71 3.2 39.5 1.0
CE1 H:HIS63 3.3 35.8 1.0
CB H:HIS63 3.3 36.0 1.0
CB H:HIS80 3.5 39.8 1.0
CB H:HIS71 3.5 36.2 1.0
CA H:HIS71 3.8 41.0 1.0
NE2 H:HIS80 4.0 38.9 1.0
O H:LYS136 4.0 38.9 1.0
CD2 H:HIS80 4.1 43.2 1.0
CB H:ASP83 4.1 37.9 1.0
NE2 H:HIS71 4.2 39.2 1.0
CD2 H:HIS71 4.3 38.7 1.0
CD2 H:HIS63 4.3 36.9 1.0
NE2 H:HIS63 4.4 37.7 1.0
N H:GLY72 4.6 40.2 1.0
CA H:ASP83 4.6 33.3 1.0
N H:ASP83 4.7 31.7 1.0
N H:HIS80 4.7 38.8 1.0
CA H:HIS80 4.7 34.1 1.0
C H:HIS71 4.7 42.5 1.0
C H:LYS136 4.9 39.4 1.0
CA H:HIS63 4.9 37.2 1.0
N H:HIS71 4.9 41.9 1.0

Zinc binding site 8 out of 9 in 6a9o

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Zinc binding site 8 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
I:Zn201

b:59.9
occ:1.00
 ND1 I:HIS63 2.2 49.5 1.0
OD1 I:ASP83 2.3 59.4 1.0
ND1 I:HIS80 2.4 52.3 1.0
ND1 I:HIS71 2.6 65.2 1.0
OD2 I:ASP83 2.9 54.6 1.0
CG I:ASP83 2.9 57.6 1.0
CG I:HIS63 3.1 52.0 1.0
CE1 I:HIS71 3.1 70.1 1.0
CG I:HIS80 3.2 52.5 1.0
CB I:HIS63 3.2 46.5 1.0
CE1 I:HIS80 3.3 53.4 1.0
CE1 I:HIS63 3.3 54.6 1.0
CB I:HIS80 3.5 47.7 1.0
CG I:HIS71 3.8 65.9 1.0
O I:LYS136 4.0 60.6 1.0
CD2 I:HIS63 4.3 53.4 1.0
CA I:HIS71 4.3 63.1 1.0
CD2 I:HIS80 4.3 51.6 1.0
CB I:ASP83 4.3 48.8 1.0
NE2 I:HIS80 4.3 53.6 1.0
CB I:HIS71 4.3 58.9 1.0
NE2 I:HIS63 4.3 51.7 1.0
NE2 I:HIS71 4.4 67.7 1.0
O I:HOH316 4.6 61.8 1.0
N I:HIS80 4.7 54.5 1.0
CD2 I:HIS71 4.7 60.5 1.0
CA I:HIS80 4.7 50.2 1.0
CA I:ASP83 4.8 49.5 1.0
CA I:HIS63 4.8 48.0 1.0
CD2 I:HIS46 4.8 50.5 1.0
N I:GLY72 5.0 60.3 1.0

Zinc binding site 9 out of 9 in 6a9o

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Zinc binding site 9 out of 9 in the Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis within 5.0Å range:
probe atom residue distance (Å) B Occ
J:Zn201

b:50.9
occ:1.00
 OD1 J:ASP83 2.0 48.4 1.0
ND1 J:HIS71 2.1 38.1 1.0
ND1 J:HIS80 2.1 38.0 1.0
ND1 J:HIS63 2.2 42.6 1.0
CG J:ASP83 2.8 43.2 1.0
CE1 J:HIS80 2.9 39.8 1.0
OD2 J:ASP83 2.9 41.7 1.0
CE1 J:HIS63 3.1 46.4 1.0
CG J:HIS71 3.1 40.5 1.0
CE1 J:HIS71 3.1 37.1 1.0
CG J:HIS80 3.1 38.8 1.0
CG J:HIS63 3.2 45.8 1.0
CB J:HIS71 3.4 42.6 1.0
CB J:HIS63 3.5 48.7 1.0
CB J:HIS80 3.6 42.1 1.0
O J:LYS136 3.6 45.3 1.0
CA J:HIS71 3.9 43.2 1.0
NE2 J:HIS80 4.0 37.7 1.0
CD2 J:HIS80 4.1 38.5 1.0
CB J:ASP83 4.1 44.1 1.0
NE2 J:HIS71 4.2 47.9 1.0
CD2 J:HIS71 4.2 39.5 1.0
NE2 J:HIS63 4.2 42.5 1.0
CD2 J:HIS63 4.3 45.3 1.0
CA J:ASP83 4.6 48.1 1.0
C J:LYS136 4.7 50.5 1.0
N J:ASP83 4.8 42.8 1.0
CA J:HIS80 4.8 42.7 1.0
O J:HOH334 4.8 44.3 1.0
N J:HIS80 4.8 41.9 1.0
C J:HIS71 4.8 45.3 1.0
N J:GLY72 4.9 41.6 1.0
CD2 J:HIS46 4.9 43.6 1.0

Reference:

R.Manjula, S.Unni, G.S.A.Wright, S.Bharath M M, B.Padmanabhan. Rational Discovery of A SOD1 Tryptophan Oxidation Inhibitor with Therapeutic Potential For Amyotrophic Lateral Sclerosis. J.Biomol.Struct.Dyn. V. 37 3936 2019.
ISSN: ESSN 1538-0254
PubMed: 30286701
DOI: 10.1080/07391102.2018.1531787
Page generated: Mon Oct 28 17:27:30 2024

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