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Sodium in PDB 7g3f: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm, PDB code: 7g3f was solved by M.Stihle, J.Benz, D.Hunziker, L.Green, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.28 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.473, 91.165, 118.586, 90, 90, 90
R / Rfree (%) 18 / 22.4

Other elements in 7g3f:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm (pdb code 7g3f). 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 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm, PDB code: 7g3f:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3f

Go back to Sodium Binding Sites List in 7g3f
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 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 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:27.9
occ:1.00
 O A:HOH1207 2.3 32.8 1.0
OG A:SER807 2.4 24.1 1.0
O A:HOH1033 2.4 29.3 1.0
O A:SER804 2.5 23.0 1.0
O A:HOH1384 2.5 35.0 1.0
O A:ASN801 2.5 19.9 1.0
C A:ASN801 3.4 21.3 1.0
CB A:SER807 3.5 28.0 1.0
C A:SER804 3.5 23.7 1.0
CA A:ASP802 3.8 23.6 1.0
N A:ASP802 4.0 21.4 1.0
O A:HOH1401 4.0 42.4 1.0
O A:HOH1101 4.1 29.3 1.0
N A:SER807 4.2 29.8 1.0
C A:ASP802 4.2 25.0 1.0
O A:ASP802 4.3 21.6 1.0
N A:CYS805 4.3 24.5 1.0
CB A:ASN801 4.3 24.7 1.0
CA A:CYS805 4.3 28.6 1.0
CA A:SER807 4.4 30.1 1.0
CA A:ASN801 4.4 23.5 1.0
OD1 A:ASP802 4.4 29.6 1.0
N A:SER804 4.4 23.4 1.0
C A:CYS805 4.5 28.6 1.0
O A:HOH1128 4.5 40.9 1.0
CA A:SER804 4.5 23.4 1.0
O A:CYS805 4.5 30.3 1.0
O A:HOH1339 4.7 36.3 1.0
CB A:SER804 4.9 24.0 1.0
N A:GLU803 5.0 23.9 1.0

Sodium binding site 2 out of 2 in 7g3f

Go back to Sodium Binding Sites List in 7g3f
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 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 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:12.9
occ:1.00
 O A:HOH1336 2.0 31.1 1.0
O A:ASP672 2.1 25.5 1.0
O A:TYR669 2.2 24.9 1.0
O A:HOH1259 2.2 33.7 1.0
O A:HOH1369 2.3 29.5 1.0
O A:MET675 2.4 25.7 1.0
C A:ASP672 3.3 28.7 1.0
C A:TYR669 3.4 28.1 1.0
C A:MET675 3.5 23.9 1.0
N A:MET675 4.2 26.4 1.0
N A:LYS673 4.2 29.2 1.0
CA A:LYS673 4.2 33.4 1.0
CA A:TYR669 4.3 26.1 1.0
N A:SER676 4.3 21.1 1.0
CA A:SER676 4.3 19.6 1.0
N A:LYS670 4.3 32.7 1.0
CA A:ASP672 4.3 30.8 1.0
O A:LYS670 4.3 33.9 1.0
CA A:MET675 4.4 24.5 1.0
C A:LYS673 4.5 32.4 1.0
CA A:LYS670 4.5 32.6 1.0
N A:ASP672 4.5 31.2 1.0
CB A:ASP672 4.6 32.1 1.0
C A:LYS670 4.6 32.1 1.0
CB A:TYR669 4.6 24.9 1.0
O A:LYS673 4.7 34.8 1.0
CB A:SER676 4.8 19.8 1.0
N A:GLN674 4.9 32.3 1.0
C A:GLN674 5.0 31.6 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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