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Sodium in PDB 7g72: Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, PDB code: 7g72 was solved by M.Stihle, J.Benz, D.Hunziker, M.Nettekoven, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.92 / 2.05
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.102, 91.847, 120.483, 90, 90, 90
R / Rfree (%) 20.1 / 25

Other elements in 7g72:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Chlorine (Cl) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide (pdb code 7g72). 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 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide, PDB code: 7g72:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g72

Go back to Sodium Binding Sites List in 7g72
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide


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 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:28.1
occ:1.00
 O A:HOH1294 2.3 26.4 1.0
O A:HOH1251 2.3 31.8 1.0
OG A:SER807 2.4 23.2 1.0
O A:SER804 2.4 28.1 1.0
O A:ASN801 2.6 20.7 1.0
O A:HOH1099 2.6 30.6 1.0
C A:SER804 3.5 29.6 1.0
CB A:SER807 3.5 26.6 1.0
C A:ASN801 3.5 22.8 1.0
CA A:ASP802 3.9 26.5 1.0
N A:SER807 4.1 28.6 1.0
N A:ASP802 4.1 23.0 1.0
CA A:CYS805 4.2 32.3 1.0
C A:ASP802 4.3 26.0 1.0
N A:CYS805 4.3 30.1 1.0
O A:ASP802 4.3 23.3 1.0
CA A:SER807 4.3 28.3 1.0
N A:SER804 4.3 25.2 1.0
C A:CYS805 4.3 31.0 1.0
O A:HOH1160 4.4 28.7 1.0
CA A:SER804 4.4 27.2 1.0
O A:CYS805 4.4 31.9 1.0
CB A:ASN801 4.4 23.3 1.0
O A:HOH1073 4.6 36.9 1.0
CA A:ASN801 4.6 23.1 1.0
OD1 A:ASP802 4.6 36.2 1.0
N A:ASN806 4.9 29.7 1.0
CB A:SER804 4.9 27.9 1.0
C A:SER807 5.0 30.6 1.0

Sodium binding site 2 out of 2 in 7g72

Go back to Sodium Binding Sites List in 7g72
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide


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 2-[6-(4- Acetylpiperazin-1-Yl)-2,4-Dioxo-1H-Quinazolin-3-Yl]-N-[(3,4- Dichlorophenyl)Methyl]Acetamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:21.2
occ:1.00
 O A:HOH1261 2.2 46.2 1.0
O A:ASP672 2.2 28.8 1.0
O A:TYR669 2.2 26.9 1.0
O A:MET675 2.3 31.9 1.0
O A:HOH1260 2.4 30.1 1.0
C A:TYR669 3.4 29.7 1.0
C A:ASP672 3.4 32.2 1.0
C A:MET675 3.4 28.6 1.0
O A:HOH1290 3.4 31.4 1.0
N A:MET675 4.1 31.5 1.0
N A:SER676 4.2 27.5 1.0
CA A:TYR669 4.2 28.1 1.0
CA A:SER676 4.3 26.9 1.0
N A:LYS673 4.3 34.6 1.0
CA A:LYS673 4.3 38.6 1.0
O A:LYS670 4.4 34.8 1.0
CA A:MET675 4.4 29.8 1.0
CA A:ASP672 4.4 31.1 1.0
N A:LYS670 4.4 32.7 1.0
C A:LYS673 4.4 39.5 1.0
N A:ASP672 4.5 35.6 1.0
CB A:ASP672 4.6 32.4 1.0
CB A:TYR669 4.6 26.6 1.0
CA A:LYS670 4.6 35.0 1.0
C A:LYS670 4.7 33.1 1.0
O A:LYS673 4.7 41.7 1.0
N A:GLN674 4.8 38.9 1.0
C A:GLN674 4.9 38.5 1.0
CB A:SER676 4.9 25.1 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 23:32:56 2025

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