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Sodium in PDB 7g4o: Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm, PDB code: 7g4o was solved by M.Stihle, J.Benz, D.Hunziker, E.Mizuguchi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.98 / 1.64
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.953, 92.017, 119.638, 90, 90, 90
R / Rfree (%) 18 / 20.9

Other elements in 7g4o:

The structure of Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm (pdb code 7g4o). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm, PDB code: 7g4o:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g4o

Go back to Sodium Binding Sites List in 7g4o
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:22.2
occ:1.00
 OG A:SER807 2.2 16.6 1.0
O A:SER804 2.3 15.8 1.0
O A:HOH1536 2.4 27.0 1.0
O A:ASN801 2.5 14.2 1.0
O A:HOH1382 2.5 25.7 1.0
O A:HOH1299 2.6 24.3 1.0
CB A:SER807 3.3 17.5 1.0
C A:ASN801 3.4 14.0 1.0
C A:SER804 3.4 18.4 1.0
CA A:ASP802 3.9 16.4 1.0
N A:SER807 4.0 19.0 1.0
N A:ASP802 4.0 14.9 1.0
CA A:SER807 4.1 18.8 1.0
CA A:CYS805 4.2 18.9 1.0
N A:CYS805 4.2 17.8 1.0
C A:CYS805 4.3 20.6 1.0
C A:ASP802 4.3 16.6 1.0
O A:ASP802 4.3 16.5 1.0
CB A:ASN801 4.3 15.5 1.0
O A:CYS805 4.3 20.1 1.0
N A:SER804 4.3 14.6 1.0
CA A:SER804 4.3 14.1 1.0
O A:HOH1184 4.4 29.0 1.0
CA A:ASN801 4.4 13.9 1.0
CB A:SER804 4.6 17.9 1.0
O A:HOH1141 4.7 27.9 1.0
OD1 A:ASP802 4.7 21.8 1.0
N A:ASN806 4.7 18.6 1.0
O A:HOH1270 4.9 27.4 1.0
C A:SER807 4.9 22.3 1.0
O A:HOH1564 5.0 38.0 1.0

Sodium binding site 2 out of 2 in 7g4o

Go back to Sodium Binding Sites List in 7g4o
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with [3-(2-Hydroxy-4,6- Dimethylphenyl)-3-Methylbutyl] 2,2-Dimethylpropanoate, I.E. Smiles C1C(Cc(C(C1O)C(Ccoc(=O)C(C)(C)C)(C)C)C)C with IC50=1.13176 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:20.4
occ:1.00
 O A:MET675 2.3 22.5 1.0
O A:ASP672 2.3 21.9 1.0
O A:TYR669 2.3 24.0 1.0
O A:HOH1374 2.4 29.4 1.0
C A:TYR669 3.4 22.2 1.0
C A:MET675 3.4 20.4 1.0
C A:ASP672 3.5 21.4 1.0
N A:MET675 4.0 20.6 1.0
CA A:TYR669 4.2 19.7 1.0
CA A:MET675 4.2 18.7 1.0
CA A:LYS673 4.3 24.9 1.0
O A:LYS670 4.3 27.6 1.0
N A:SER676 4.3 17.3 1.0
N A:LYS673 4.4 20.2 1.0
CA A:SER676 4.4 17.1 1.0
C A:LYS673 4.4 23.4 1.0
N A:LYS670 4.4 23.1 1.0
CA A:ASP672 4.4 21.2 1.0
N A:ASP672 4.5 23.1 1.0
CB A:TYR669 4.5 19.1 1.0
O A:HOH1575 4.5 32.1 1.0
C A:LYS670 4.5 25.0 1.0
CA A:LYS670 4.6 25.4 1.0
CB A:ASP672 4.6 20.4 1.0
O A:LYS673 4.7 26.9 1.0
N A:GLN674 4.8 22.1 1.0
CB A:MET675 4.9 18.2 1.0
C A:GLN674 5.0 23.7 1.0

Reference:

D.Hunziker, S.C.Joachim, C.Ullmer, M.G.Rudolph. Crystal Structure of A Rat Autotaxin Complex To Be Published.
Page generated: Sat Feb 8 23:18:33 2025

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