Atomistry » Sodium » PDB 5rdn-5syl » 5s9l
Atomistry »
  Sodium »
    PDB 5rdn-5syl »
      5s9l »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy