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Sodium in PDB 5s9l: Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1%

Enzymatic activity of Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1%

All present enzymatic activity of Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1%, PDB code: 5s9l 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) 61.70 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.543, 91.259, 118.405, 90, 90, 90
R / Rfree (%) 15.8 / 19.1

Other elements in 5s9l:

The structure of Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1% also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1% (pdb code 5s9l). 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-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1%, PDB code: 5s9l:

Sodium binding site 1 out of 1 in 5s9l

Go back to Sodium Binding Sites List in 5s9l
Sodium binding site 1 out of 1 in the Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1%


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Autotaxin, 4-[3-Oxo-3-(2-Oxo-2,3-Dihydro-Benzooxazol-6-Yl)-Propyl]- Piperazine-1-Carboxylic Acid 3,5-Dichloro-Benzyl Ester, 1.90A, P212121, Rfree=19.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:28.8
occ:1.00
 O A:HOH1267 2.3 28.3 1.0
O A:SER804 2.3 24.9 1.0
OG A:SER807 2.3 25.9 1.0
O A:HOH1456 2.4 35.9 1.0
O A:ASN801 2.4 23.4 1.0
O A:HOH1085 2.5 32.4 1.0
C A:ASN801 3.3 24.0 1.0
C A:SER804 3.4 23.7 1.0
CB A:SER807 3.4 27.0 1.0
CA A:ASP802 3.8 25.4 1.0
N A:ASP802 3.9 24.1 1.0
N A:SER807 4.1 27.6 1.0
O A:ASP802 4.2 24.2 1.0
O A:HOH1019 4.2 38.0 1.0
N A:CYS805 4.2 25.6 1.0
C A:ASP802 4.2 25.1 1.0
CA A:CYS805 4.2 28.6 1.0
CA A:SER807 4.3 29.3 1.0
N A:SER804 4.3 22.6 1.0
CA A:SER804 4.3 22.6 1.0
C A:CYS805 4.4 29.3 1.0
CB A:ASN801 4.4 23.6 1.0
CA A:ASN801 4.4 24.0 1.0
O A:CYS805 4.4 32.0 1.0
OD1 A:ASP802 4.5 32.5 1.0
O A:HOH1192 4.7 37.4 1.0
CB A:SER804 4.7 24.2 1.0
N A:ASN806 4.9 29.2 1.0
O A:HOH1329 4.9 34.0 1.0
N A:GLU803 5.0 22.4 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: Mon Oct 7 23:54:08 2024

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