Atomistry » Sodium » PDB 7g4c-7g5v » 7g4r
Atomistry »
  Sodium »
    PDB 7g4c-7g5v »
      7g4r »

Sodium in PDB 7g4r: Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm, PDB code: 7g4r was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.48 / 2.09
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.497, 92.96, 120.809, 90, 90, 90
R / Rfree (%) 18.3 / 22

Other elements in 7g4r:

The structure of Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm (pdb code 7g4r). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm, PDB code: 7g4r:

Sodium binding site 1 out of 1 in 7g4r

Go back to Sodium Binding Sites List in 7g4r
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with (3-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 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-Chloro-5- Methylsulfonylphenyl)Methyl Rac-(3AR,8AS)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, I.E. Smiles N1(Cc[C@@H]2[C@H](CC1)Cn(C2)C(=O) C1CCC2C(C1)N=NN2)C(=O)OCC1CC(Cc(C1)Cl)S(=O)(=O)C with IC50=0.00849941 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:46.1
occ:1.00
 O A:ASP672 2.3 41.2 1.0
O A:TYR669 2.3 45.9 1.0
O A:MET675 2.3 42.5 1.0
O A:HOH1378 2.5 44.9 1.0
C A:MET675 3.4 35.1 1.0
C A:ASP672 3.4 43.4 1.0
C A:TYR669 3.5 47.6 1.0
N A:MET675 4.1 42.6 1.0
CA A:LYS673 4.1 51.1 1.0
N A:SER676 4.2 36.8 1.0
CA A:TYR669 4.2 40.6 1.0
N A:LYS673 4.2 48.5 1.0
C A:LYS673 4.3 47.1 1.0
CA A:MET675 4.3 37.6 1.0
CA A:SER676 4.3 37.1 1.0
O A:HOH1347 4.4 51.2 1.0
CA A:ASP672 4.4 44.4 1.0
O A:LYS673 4.4 43.3 1.0
O A:LYS670 4.4 52.0 1.0
N A:LYS670 4.5 50.3 1.0
N A:ASP672 4.6 54.5 1.0
CB A:TYR669 4.6 38.5 1.0
C A:LYS670 4.7 46.7 1.0
CA A:LYS670 4.7 48.6 1.0
CB A:ASP672 4.7 42.0 1.0
N A:GLN674 4.7 45.8 1.0
C A:GLN674 5.0 43.4 1.0
CB A:SER676 5.0 31.2 1.0
CB A:MET675 5.0 37.4 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: Mon Aug 18 09:58:43 2025

Last articles

Na in 7YQN
Na in 7YQS
Na in 7YF7
Na in 7YQ0
Na in 7YPY
Na in 7YPZ
Na in 7YNH
Na in 7YNV
Na in 7YNU
Na in 7YNE
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy