Atomistry » Sodium » PDB 7g33-7g48 » 7g3a
Atomistry »
  Sodium »
    PDB 7g33-7g48 »
      7g3a »

Sodium in PDB 7g3a: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm, PDB code: 7g3a 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) 45.91 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.858, 91.826, 119.462, 90, 90, 90
R / Rfree (%) 18.8 / 22.6

Other elements in 7g3a:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 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 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm (pdb code 7g3a). 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 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm, PDB code: 7g3a:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g3a

Go back to Sodium Binding Sites List in 7g3a
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 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 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:30.8
occ:1.00
 OG A:SER807 2.3 24.6 1.0
O A:HOH1415 2.4 30.5 1.0
O A:SER804 2.4 22.2 1.0
O A:HOH1205 2.5 37.3 1.0
O A:ASN801 2.6 21.4 1.0
O A:HOH1292 2.6 29.8 1.0
CB A:SER807 3.4 23.7 1.0
C A:ASN801 3.4 21.8 1.0
C A:SER804 3.5 22.2 1.0
CA A:ASP802 3.9 25.4 1.0
N A:SER807 4.1 26.6 1.0
N A:ASP802 4.1 21.6 1.0
O A:HOH1055 4.1 35.7 1.0
CA A:CYS805 4.2 26.0 1.0
CA A:SER807 4.2 27.0 1.0
O A:ASP802 4.2 23.3 1.0
C A:ASP802 4.3 22.9 1.0
N A:CYS805 4.3 24.6 1.0
C A:CYS805 4.3 28.3 1.0
CB A:ASN801 4.4 22.0 1.0
CA A:SER804 4.4 19.6 1.0
N A:SER804 4.4 19.9 1.0
O A:CYS805 4.4 29.1 1.0
CA A:ASN801 4.5 21.4 1.0
O A:HOH1206 4.6 29.8 1.0
CB A:SER804 4.7 21.0 1.0
OD1 A:ASP802 4.8 28.6 1.0
N A:ASN806 4.9 26.2 1.0
O A:HOH1148 4.9 34.4 1.0
C A:SER807 5.0 28.7 1.0

Sodium binding site 2 out of 2 in 7g3a

Go back to Sodium Binding Sites List in 7g3a
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 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 5-Tert-Butyl-2- Methyl-4-[(5-Oxo-4-Propan-2-Yl-1H-1,2,4-Triazol-3-Yl) Methoxy]Benzonitrile, I.E. Smiles C(C1=Nnc(=O)N1C(C)C) OC1CC(C(CC1C(C)(C)C)C#N)C with IC50=0.0371228 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:29.7
occ:1.00
 O A:MET675 2.3 25.6 1.0
O A:ASP672 2.3 31.0 1.0
O A:TYR669 2.3 27.1 1.0
O A:HOH1397 2.3 35.2 1.0
C A:MET675 3.4 24.5 1.0
C A:TYR669 3.4 29.0 1.0
C A:ASP672 3.5 32.1 1.0
N A:MET675 4.0 25.8 1.0
CA A:TYR669 4.2 25.1 1.0
CA A:MET675 4.3 23.8 1.0
O A:HOH1446 4.3 39.9 1.0
N A:SER676 4.3 19.1 1.0
O A:LYS670 4.3 38.7 1.0
CA A:SER676 4.4 20.4 1.0
CA A:ASP672 4.4 31.0 1.0
CA A:LYS673 4.4 34.8 1.0
N A:LYS673 4.4 31.1 1.0
C A:LYS673 4.4 30.6 1.0
N A:LYS670 4.4 29.1 1.0
N A:ASP672 4.5 33.9 1.0
CB A:TYR669 4.5 23.7 1.0
CB A:ASP672 4.6 27.6 1.0
C A:LYS670 4.6 33.6 1.0
O A:LYS673 4.6 31.1 1.0
CA A:LYS670 4.7 33.7 1.0
N A:GLN674 4.8 28.0 1.0
CB A:MET675 4.8 24.8 1.0
CB A:SER676 4.9 19.6 1.0
C A:GLN674 5.0 28.1 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

Last articles

Zn in 9IRQ
Zn in 9IYX
Zn in 9J8P
Zn in 9IUU
Zn in 9GBF
Zn in 9G2V
Zn in 9G2L
Zn in 9G2X
Zn in 9G2Z
Zn in 9G2K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy