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Sodium in PDB 5s9m: Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%

Enzymatic activity of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%

All present enzymatic activity of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%, PDB code: 5s9m 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) 48.37 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.017, 91.009, 119.028, 90, 90, 90
R / Rfree (%) 17.1 / 21.1

Other elements in 5s9m:

The structure of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% (pdb code 5s9m). 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, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%, PDB code: 5s9m:

Sodium binding site 1 out of 1 in 5s9m

Go back to Sodium Binding Sites List in 5s9m
Sodium binding site 1 out of 1 in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na913

b:40.8
occ:1.00
 OG A:SER807 2.2 23.5 1.0
O A:SER804 2.4 25.8 1.0
O A:HOH1308 2.5 45.0 1.0
O A:ASN801 2.5 21.3 1.0
O A:HOH1448 2.5 39.0 1.0
O A:HOH1049 2.7 36.8 1.0
C A:ASN801 3.3 23.3 1.0
CB A:SER807 3.4 25.9 1.0
C A:SER804 3.4 26.4 1.0
CA A:ASP802 3.8 25.2 1.0
O A:HOH1017 3.8 37.8 1.0
N A:ASP802 3.9 23.2 1.0
N A:SER807 4.0 26.9 1.0
C A:ASP802 4.2 23.5 1.0
O A:ASP802 4.2 24.4 1.0
CA A:SER807 4.2 27.4 1.0
CA A:CYS805 4.3 29.0 1.0
N A:CYS805 4.3 27.2 1.0
CB A:ASN801 4.3 23.0 1.0
N A:SER804 4.3 21.8 1.0
CA A:SER804 4.3 22.7 1.0
C A:CYS805 4.3 29.6 1.0
O A:CYS805 4.4 33.0 1.0
CA A:ASN801 4.4 23.0 1.0
OD1 A:ASP802 4.6 35.3 1.0
O A:HOH1103 4.6 36.0 1.0
CB A:SER804 4.7 21.5 1.0
O A:HOH1098 4.7 38.1 1.0
C A:SER807 4.8 31.9 1.0
N A:ASN806 4.9 28.9 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: Mon Oct 7 23:54:08 2024

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