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Sodium in PDB 7g7z: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid, PDB code: 7g7z was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.096, 92.112, 120.482, 90, 90, 90
R / Rfree (%) 20.2 / 24.2

Other elements in 7g7z:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Fluorine (F) 7 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid (pdb code 7g7z). 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-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid, PDB code: 7g7z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g7z

Go back to Sodium Binding Sites List in 7g7z
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid


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-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:33.0
occ:1.00
 O A:HOH1380 2.2 39.5 1.0
O A:SER804 2.3 32.4 1.0
OG A:SER807 2.3 34.2 1.0
O A:HOH1322 2.4 40.3 1.0
O A:HOH1084 2.4 35.8 1.0
O A:ASN801 2.5 28.7 1.0
C A:SER804 3.3 33.1 1.0
C A:ASN801 3.4 26.0 1.0
CB A:SER807 3.4 34.2 1.0
CA A:ASP802 3.8 31.4 1.0
N A:ASP802 4.0 27.9 1.0
N A:CYS805 4.1 32.9 1.0
CA A:CYS805 4.1 35.6 1.0
N A:SER807 4.1 34.3 1.0
C A:ASP802 4.2 30.8 1.0
O A:ASP802 4.2 30.8 1.0
CA A:SER807 4.3 34.6 1.0
C A:CYS805 4.3 36.5 1.0
CA A:SER804 4.3 29.9 1.0
N A:SER804 4.3 28.4 1.0
CB A:ASN801 4.4 27.8 1.0
CA A:ASN801 4.5 28.7 1.0
O A:CYS805 4.5 40.9 1.0
OD1 A:ASP802 4.6 35.9 1.0
O A:HOH1170 4.7 35.5 1.0
CB A:SER804 4.8 30.5 1.0
O A:HOH1263 4.9 39.3 1.0
N A:ASN806 4.9 35.4 1.0
N A:GLU803 5.0 27.6 1.0

Sodium binding site 2 out of 2 in 7g7z

Go back to Sodium Binding Sites List in 7g7z
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid


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-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:25.6
occ:1.00
 O A:ASP672 2.2 34.8 1.0
O A:HOH1364 2.2 43.8 1.0
O A:MET675 2.3 34.8 1.0
O A:HOH1307 2.3 42.0 1.0
O A:TYR669 2.3 33.9 1.0
C A:MET675 3.4 35.8 1.0
C A:ASP672 3.4 38.0 1.0
C A:TYR669 3.5 36.9 1.0
N A:MET675 4.1 39.3 1.0
N A:SER676 4.2 31.2 1.0
N A:LYS673 4.3 39.9 1.0
CA A:TYR669 4.3 34.1 1.0
CA A:SER676 4.3 30.1 1.0
CA A:LYS673 4.3 43.6 1.0
CA A:MET675 4.3 36.2 1.0
O A:LYS670 4.3 40.4 1.0
CA A:ASP672 4.4 38.5 1.0
C A:LYS673 4.4 43.7 1.0
N A:LYS670 4.5 40.3 1.0
N A:ASP672 4.5 41.1 1.0
CB A:ASP672 4.5 38.6 1.0
O A:LYS673 4.6 41.6 1.0
C A:LYS670 4.6 38.5 1.0
CA A:LYS670 4.6 41.1 1.0
CB A:TYR669 4.7 31.8 1.0
N A:GLN674 4.8 42.1 1.0
CB A:SER676 4.9 31.7 1.0
C A:GLN674 5.0 41.7 1.0
CB A:MET675 5.0 35.1 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 23:37:45 2025

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