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Sodium in PDB 7g6g: Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine:
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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine, PDB code: 7g6g 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) 45.94 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.98, 91.888, 119.682, 90, 90, 90
R / Rfree (%) 19 / 23.3

Other elements in 7g6g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine also contains other interesting chemical elements:

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

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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine (pdb code 7g6g). 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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine, PDB code: 7g6g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6g

Go back to Sodium Binding Sites List in 7g6g
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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine


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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:29.4
occ:1.00
 OG A:SER807 2.3 22.2 1.0
O A:HOH1427 2.4 27.1 1.0
O A:HOH1209 2.4 31.4 1.0
O A:HOH1359 2.4 25.6 1.0
O A:SER804 2.4 22.3 1.0
O A:ASN801 2.5 20.9 1.0
C A:ASN801 3.4 22.0 1.0
CB A:SER807 3.5 24.0 1.0
C A:SER804 3.5 23.0 1.0
CA A:ASP802 3.8 24.2 1.0
N A:ASP802 4.0 21.3 1.0
N A:SER807 4.1 25.9 1.0
O A:ASP802 4.2 23.1 1.0
C A:ASP802 4.2 21.8 1.0
O A:HOH1078 4.3 37.2 1.0
CA A:CYS805 4.3 26.2 1.0
N A:CYS805 4.3 23.4 1.0
CA A:SER807 4.3 26.7 1.0
CB A:ASN801 4.3 21.8 1.0
CA A:ASN801 4.4 21.5 1.0
C A:CYS805 4.4 27.2 1.0
N A:SER804 4.4 20.3 1.0
CA A:SER804 4.5 21.4 1.0
O A:CYS805 4.5 28.4 1.0
O A:HOH1167 4.7 31.2 1.0
OD1 A:ASP802 4.7 30.1 1.0
O A:HOH1273 4.8 31.7 1.0
CB A:SER804 4.8 23.0 1.0
N A:ASN806 5.0 26.1 1.0

Sodium binding site 2 out of 2 in 7g6g

Go back to Sodium Binding Sites List in 7g6g
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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine


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]-4,5,6,7-Tetrahydro-1H-Pyrazolo[4,3- C]Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:30.4
occ:1.00
 O A:MET675 2.3 26.0 1.0
O A:ASP672 2.3 30.3 1.0
O A:TYR669 2.4 27.6 1.0
O A:HOH1403 2.4 34.0 1.0
O A:HOH1455 3.2 38.6 1.0
C A:MET675 3.4 25.2 1.0
C A:ASP672 3.5 31.6 1.0
C A:TYR669 3.5 28.2 1.0
N A:MET675 4.1 28.9 1.0
CA A:TYR669 4.2 24.8 1.0
CA A:MET675 4.3 24.9 1.0
O A:LYS670 4.3 30.9 1.0
CA A:LYS673 4.3 33.9 1.0
N A:SER676 4.3 21.6 1.0
N A:LYS673 4.4 31.8 1.0
CA A:ASP672 4.4 29.8 1.0
CA A:SER676 4.4 21.8 1.0
C A:LYS673 4.4 31.5 1.0
N A:LYS670 4.5 28.5 1.0
N A:ASP672 4.5 32.0 1.0
CB A:TYR669 4.5 24.1 1.0
CB A:ASP672 4.6 27.1 1.0
O A:LYS673 4.6 29.2 1.0
C A:LYS670 4.6 31.1 1.0
CA A:LYS670 4.7 32.7 1.0
N A:GLN674 4.9 29.6 1.0
CB A:MET675 4.9 23.0 1.0
C A:GLN674 5.0 31.1 1.0
CB A:SER676 5.0 21.7 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 23:28:34 2025

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