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Sodium in PDB 5s9n: Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%

Enzymatic activity of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%

All present enzymatic activity of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%, PDB code: 5s9n was solved by M.Stihle, D.Hunziker, J.Benz, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.114, 91.731, 120.21, 90, 90, 90
R / Rfree (%) 19.1 / 23.3

Other elements in 5s9n:

The structure of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom
Calcium (Ca) 2 atoms
Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% (pdb code 5s9n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%, PDB code: 5s9n:

Sodium binding site 1 out of 1 in 5s9n

Go back to Sodium Binding Sites List in 5s9n
Sodium binding site 1 out of 1 in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na909

b:35.0
occ:1.00
 OG A:SER807 2.3 27.8 1.0
O A:SER804 2.3 23.7 1.0
O A:HOH1245 2.5 33.4 1.0
O A:HOH1370 2.5 35.8 1.0
O A:ASN801 2.5 26.1 1.0
O A:HOH1128 2.6 32.6 1.0
C A:ASN801 3.3 22.3 1.0
CB A:SER807 3.4 27.6 1.0
C A:SER804 3.4 23.6 1.0
CA A:ASP802 3.8 26.7 1.0
N A:ASP802 4.0 24.0 1.0
N A:SER807 4.0 30.8 1.0
O A:HOH1019 4.2 41.2 1.0
C A:ASP802 4.2 25.1 1.0
O A:ASP802 4.2 25.7 1.0
CA A:SER807 4.2 27.6 1.0
CA A:CYS805 4.2 30.4 1.0
N A:CYS805 4.2 26.8 1.0
N A:SER804 4.3 20.9 1.0
CB A:ASN801 4.3 22.4 1.0
CA A:SER804 4.3 21.2 1.0
CA A:ASN801 4.4 22.9 1.0
C A:CYS805 4.4 29.4 1.0
O A:CYS805 4.5 32.6 1.0
CB A:SER804 4.6 22.3 1.0
O A:HOH1163 4.6 36.1 1.0
OD1 A:ASP802 4.7 36.8 1.0
O A:HOH1173 4.8 38.5 1.0
N A:ASN806 4.9 31.7 1.0
N A:GLU803 4.9 22.5 1.0
C A:SER807 5.0 31.4 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: Fri Apr 7 14:29:03 2023

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