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Sodium in PDB 7g3b: Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm, PDB code: 7g3b was solved by M.Stihle, J.Benz, D.Hunziker, H.Richter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.88 / 1.56
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.149, 91.841, 119.912, 90, 90, 90
R / Rfree (%) 18.2 / 21.3

Other elements in 7g3b:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm (pdb code 7g3b). 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-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm, PDB code: 7g3b:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3b

Go back to Sodium Binding Sites List in 7g3b
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 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-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:23.5
occ:1.00
 OG A:SER807 2.2 21.0 1.0
O A:SER804 2.4 20.8 1.0
O A:ASN801 2.4 18.5 1.0
O A:HOH1481 2.4 33.0 1.0
O A:HOH1354 2.5 27.3 1.0
O A:HOH1386 2.5 28.3 1.0
C A:ASN801 3.3 16.7 1.0
CB A:SER807 3.3 22.1 1.0
C A:SER804 3.4 18.2 1.0
CA A:ASP802 3.8 20.4 1.0
N A:ASP802 4.0 18.1 1.0
N A:SER807 4.0 22.6 1.0
CA A:SER807 4.2 23.2 1.0
C A:ASP802 4.2 18.5 1.0
CA A:CYS805 4.2 20.1 1.0
O A:ASP802 4.3 20.3 1.0
O A:HOH1138 4.3 31.6 1.0
CB A:ASN801 4.3 17.5 1.0
N A:CYS805 4.3 17.8 1.0
N A:SER804 4.3 15.9 1.0
C A:CYS805 4.3 23.2 1.0
CA A:ASN801 4.4 17.4 1.0
CA A:SER804 4.4 15.6 1.0
O A:CYS805 4.4 25.4 1.0
CB A:SER804 4.6 19.0 1.0
O A:HOH1122 4.7 29.3 1.0
OD1 A:ASP802 4.7 28.3 1.0
O A:HOH1315 4.8 30.5 1.0
N A:ASN806 4.9 21.7 1.0
C A:SER807 5.0 26.1 1.0
N A:GLU803 5.0 17.5 1.0

Sodium binding site 2 out of 2 in 7g3b

Go back to Sodium Binding Sites List in 7g3b
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 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-Tert-Butyl-4- Methylsulfonylphenoxy)Methyl]-4-Methyl-1H-1,2,4-Triazol-5-One, I.E. Smiles O(C1CCC(CC1C(C)(C)C)S(=O)(=O)C)CC1=Nnc(=O)N1C with IC50=3.84238 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:22.8
occ:1.00
 O A:MET675 2.3 23.9 1.0
O A:TYR669 2.3 25.3 1.0
O A:ASP672 2.3 26.4 1.0
O A:HOH1368 2.4 32.1 1.0
O A:HOH1499 2.9 42.1 1.0
C A:TYR669 3.4 25.7 1.0
C A:MET675 3.4 22.3 1.0
C A:ASP672 3.5 22.4 1.0
N A:MET675 4.0 22.3 1.0
CA A:TYR669 4.2 21.8 1.0
CA A:MET675 4.3 21.0 1.0
CA A:LYS673 4.3 26.9 1.0
O A:LYS670 4.3 32.2 1.0
N A:SER676 4.3 18.2 1.0
C A:LYS673 4.4 26.6 1.0
N A:LYS670 4.4 25.1 1.0
N A:LYS673 4.4 26.4 1.0
CA A:SER676 4.4 18.8 1.0
CA A:ASP672 4.4 24.6 1.0
N A:ASP672 4.4 26.4 1.0
CB A:ASP672 4.5 23.2 1.0
CB A:TYR669 4.5 21.5 1.0
O A:HOH1520 4.5 41.9 1.0
C A:LYS670 4.6 27.7 1.0
O A:LYS673 4.6 27.9 1.0
CA A:LYS670 4.6 29.5 1.0
N A:GLN674 4.8 25.1 1.0
CB A:MET675 4.9 19.8 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 23:12:39 2025

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