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Sodium in PDB 7g6h: Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm, PDB code: 7g6h was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.57 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.855, 91.412, 119.157, 90, 90, 90
R / Rfree (%) 19 / 24.3

Other elements in 7g6h:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms
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- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm (pdb code 7g6h). 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- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm, PDB code: 7g6h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6h

Go back to Sodium Binding Sites List in 7g6h
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 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- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:34.7
occ:1.00
 OG A:SER807 2.2 32.6 1.0
O A:HOH1251 2.3 37.9 1.0
O A:SER804 2.3 31.2 1.0
O A:HOH1396 2.4 43.7 1.0
O A:HOH1299 2.5 37.0 1.0
O A:ASN801 2.6 26.6 1.0
C A:SER804 3.4 32.7 1.0
CB A:SER807 3.4 31.8 1.0
C A:ASN801 3.5 28.7 1.0
CA A:ASP802 4.0 33.6 1.0
N A:SER807 4.0 33.9 1.0
N A:ASP802 4.1 30.3 1.0
O A:ASP802 4.1 30.8 1.0
CA A:CYS805 4.2 38.4 1.0
N A:CYS805 4.2 33.1 1.0
CA A:SER807 4.2 35.3 1.0
C A:ASP802 4.2 35.5 1.0
C A:CYS805 4.3 36.2 1.0
N A:SER804 4.3 30.7 1.0
CA A:SER804 4.3 31.8 1.0
CB A:ASN801 4.3 29.0 1.0
O A:CYS805 4.4 36.2 1.0
CA A:ASN801 4.5 30.1 1.0
CB A:SER804 4.7 32.0 1.0
N A:ASN806 4.8 36.6 1.0
OD1 A:ASP802 4.8 46.6 1.0
O A:HOH1194 4.8 48.3 1.0
C A:SER807 4.9 38.9 1.0

Sodium binding site 2 out of 2 in 7g6h

Go back to Sodium Binding Sites List in 7g6h
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 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- Chloro-5-Methylphenoxy)Methyl]-1H-Pyrazole, I.E. Smiles O(C1CC(C(CC1C(C)(C)C)Cl)C)CC1=Nnc=C1 with IC50=0.0632907 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:22.8
occ:1.00
 O A:HOH1374 2.1 42.6 1.0
O A:ASP672 2.2 35.0 1.0
O A:TYR669 2.2 37.4 1.0
O A:HOH1343 2.3 33.5 1.0
O A:MET675 2.4 36.6 1.0
O A:HOH1402 2.5 46.7 1.0
C A:ASP672 3.4 35.6 1.0
C A:TYR669 3.4 38.5 1.0
C A:MET675 3.5 34.4 1.0
N A:MET675 4.1 35.9 1.0
N A:LYS673 4.3 37.2 1.0
CA A:TYR669 4.3 34.0 1.0
CA A:LYS673 4.3 41.9 1.0
CA A:ASP672 4.3 36.0 1.0
CA A:MET675 4.4 34.0 1.0
N A:SER676 4.4 30.9 1.0
C A:LYS673 4.4 40.9 1.0
O A:LYS670 4.4 40.1 1.0
CA A:SER676 4.4 27.8 1.0
N A:LYS670 4.4 39.5 1.0
N A:ASP672 4.5 40.0 1.0
CB A:ASP672 4.5 36.9 1.0
O A:LYS673 4.6 43.2 1.0
CA A:LYS670 4.6 42.4 1.0
C A:LYS670 4.7 39.8 1.0
CB A:TYR669 4.7 31.4 1.0
N A:GLN674 4.8 41.5 1.0
C A:GLN674 5.0 41.0 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 23:28:33 2025

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