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Calcium 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
Potassium (K) 1 atom
Sodium (Na) 1 atom

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where 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:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5s9l

Go back to Calcium Binding Sites List in 5s9l
Calcium binding site 1 out of 2 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 Calcium with other atoms in the Ca 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:Ca901

b:52.2
occ:1.00
 OD1 A:ASP171 2.1 28.3 1.0
NE2 A:HIS359 2.3 19.2 1.0
OD2 A:ASP358 2.4 24.0 1.0
OG1 A:THR209 2.8 29.4 1.0
CG A:ASP171 2.9 26.9 1.0
CG2 A:THR209 3.1 28.0 1.0
CE1 A:HIS359 3.1 20.8 1.0
CB A:THR209 3.1 26.6 1.0
OD2 A:ASP171 3.2 35.8 1.0
CG A:ASP358 3.3 21.4 1.0
CD2 A:HIS359 3.3 20.2 1.0
CA A:THR209 3.3 22.2 1.0
OD1 A:ASP358 3.6 18.3 1.0
N A:THR209 3.9 19.9 1.0
OD1 A:ASP311 4.0 24.5 1.0
C27 A:6ZO906 4.1 28.2 1.0
CE1 A:HIS474 4.1 17.6 1.0
ND1 A:HIS359 4.2 18.7 1.0
ZN A:ZN907 4.3 21.4 1.0
CB A:ASP171 4.3 23.2 1.0
CG A:HIS359 4.3 18.4 1.0
NE2 A:HIS474 4.3 18.1 1.0
CG A:ASP311 4.4 23.5 1.0
N A:GLY172 4.4 20.7 1.0
C28 A:6ZO906 4.4 27.7 1.0
N31 A:6ZO906 4.5 23.5 1.0
CB A:ASP358 4.5 18.6 1.0
CA A:ASP171 4.6 21.6 1.0
C A:THR209 4.6 20.1 1.0
C A:LYS208 4.6 20.2 1.0
OD2 A:ASP311 4.8 31.2 1.0
C25 A:6ZO906 4.9 28.0 1.0
CB A:ASP311 4.9 20.7 1.0
C A:ASP171 4.9 22.3 1.0
ND1 A:HIS474 4.9 18.3 1.0
O A:THR209 5.0 19.2 1.0

Calcium binding site 2 out of 2 in 5s9l

Go back to Calcium Binding Sites List in 5s9l
Calcium binding site 2 out of 2 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 Calcium with other atoms in the Ca binding site number 2 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:Ca909

b:19.4
occ:1.00
 OD1 A:ASP747 2.3 20.2 1.0
O A:LEU745 2.3 20.9 1.0
OD1 A:ASP739 2.3 17.7 1.0
OD1 A:ASN741 2.3 19.5 1.0
OD1 A:ASP743 2.4 20.4 1.0
O A:HOH1425 2.4 21.4 1.0
CG A:ASP743 3.3 21.2 1.0
CG A:ASN741 3.4 23.3 1.0
C A:LEU745 3.5 18.5 1.0
CG A:ASP739 3.5 19.7 1.0
CG A:ASP747 3.5 20.4 1.0
OD2 A:ASP743 3.8 21.7 1.0
ND2 A:ASN741 3.8 23.7 1.0
N A:ASP747 3.9 18.0 1.0
CA A:ASP739 3.9 19.1 1.0
C A:ARG746 4.0 19.3 1.0
N A:LEU745 4.1 17.7 1.0
CA A:ASP747 4.1 19.5 1.0
O A:ARG746 4.2 17.6 1.0
CB A:ASP739 4.2 18.6 1.0
CA A:LEU745 4.2 18.8 1.0
N A:ASP743 4.3 18.6 1.0
OD2 A:ASP747 4.4 23.1 1.0
OD2 A:ASP739 4.4 18.9 1.0
CB A:ASP747 4.4 20.1 1.0
O A:PHE738 4.4 18.8 1.0
N A:ARG746 4.5 18.3 1.0
C A:ASP739 4.5 19.1 1.0
CB A:LEU745 4.5 19.5 1.0
CB A:ASP743 4.5 21.2 1.0
N A:ASN741 4.5 19.9 1.0
O A:HOH1305 4.6 39.4 1.0
OE2 A:GLU751 4.7 34.5 1.0
CB A:ASN741 4.7 21.1 1.0
N A:TYR740 4.7 20.2 1.0
CA A:ARG746 4.8 19.9 1.0
N A:TYR742 4.8 20.1 1.0
CA A:ASP743 4.8 19.5 1.0
N A:GLY744 4.9 20.0 1.0
C A:ASN741 4.9 21.3 1.0
CA A:ASN741 4.9 21.4 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: Wed Jul 9 09:45:24 2025

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