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Sodium in PDB 7g67: Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One, PDB code: 7g67 was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.11 / 1.97
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.629, 92.367, 120.587, 90, 90, 90
R / Rfree (%) 20.1 / 23.9

Other elements in 7g67:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 3 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-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One (pdb code 7g67). 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-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One, PDB code: 7g67:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g67

Go back to Sodium Binding Sites List in 7g67
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One


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-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:44.8
occ:1.00
 O A:HOH1214 2.3 46.9 1.0
OG A:SER807 2.4 36.4 1.0
O A:HOH1084 2.5 48.5 1.0
O A:SER804 2.5 37.0 1.0
O A:ASN801 2.7 31.7 1.0
C A:ASN801 3.5 32.3 1.0
CB A:SER807 3.5 35.4 1.0
C A:SER804 3.6 39.8 1.0
CA A:ASP802 3.9 36.5 1.0
N A:ASP802 4.1 35.9 1.0
N A:SER807 4.2 41.0 1.0
C A:ASP802 4.3 36.7 1.0
O A:ASP802 4.3 35.4 1.0
CA A:SER807 4.4 40.7 1.0
CA A:CYS805 4.4 44.2 1.0
N A:CYS805 4.4 42.8 1.0
CB A:ASN801 4.4 30.8 1.0
C A:CYS805 4.5 43.0 1.0
O A:CYS805 4.5 46.0 1.0
CA A:ASN801 4.5 32.4 1.0
N A:SER804 4.6 35.3 1.0
O A:HOH1077 4.6 39.8 1.0
CA A:SER804 4.6 36.4 1.0
O A:HOH1101 4.6 38.5 1.0
OD1 A:ASP802 4.7 38.6 1.0
CB A:SER804 5.0 37.4 1.0
C A:SER807 5.0 43.1 1.0

Sodium binding site 2 out of 2 in 7g67

Go back to Sodium Binding Sites List in 7g67
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One


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-(1- Acetylpiperidin-4-Yl)-4-[(E)-(4-Chlorophenyl)Diazenyl]-1,4- Dihydropyrazol-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:30.6
occ:1.00
 O A:ASP672 2.2 42.3 1.0
O A:MET675 2.3 38.3 1.0
O A:HOH1290 2.3 40.6 1.0
O A:TYR669 2.3 44.1 1.0
O A:HOH1298 2.5 48.6 1.0
O A:HOH1307 2.7 47.8 1.0
C A:MET675 3.4 37.3 1.0
C A:ASP672 3.4 43.9 1.0
C A:TYR669 3.5 42.7 1.0
N A:MET675 4.2 41.6 1.0
N A:SER676 4.3 34.9 1.0
CA A:LYS673 4.3 48.6 1.0
CA A:TYR669 4.3 39.4 1.0
N A:LYS673 4.3 44.8 1.0
CA A:SER676 4.4 34.0 1.0
CA A:MET675 4.4 38.2 1.0
C A:LYS673 4.4 46.6 1.0
CA A:ASP672 4.4 43.4 1.0
N A:LYS670 4.5 46.6 1.0
O A:LYS673 4.6 45.5 1.0
O A:LYS670 4.6 48.4 1.0
CB A:ASP672 4.6 43.6 1.0
CB A:TYR669 4.7 37.0 1.0
CA A:LYS670 4.7 48.8 1.0
N A:ASP672 4.7 47.0 1.0
C A:LYS670 4.8 46.5 1.0
N A:GLN674 4.8 43.7 1.0
CB A:SER676 4.9 33.9 1.0
C A:GLN674 4.9 45.2 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 23:25:46 2025

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