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Zinc 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
Calcium (Ca) 2 atoms
Potassium (K) 1 atom
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc 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:

Zinc binding site 1 out of 1 in 5s9l

Go back to Zinc Binding Sites List in 5s9l
Zinc 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 Zinc with other atoms in the Zn 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:Zn907

b:21.4
occ:1.00
 N31 A:6ZO906 2.0 23.5 1.0
NE2 A:HIS474 2.0 18.1 1.0
NE2 A:HIS315 2.1 21.8 1.0
OD1 A:ASP311 2.1 24.5 1.0
OD2 A:ASP311 2.5 31.2 1.0
CG A:ASP311 2.6 23.5 1.0
C30 A:6ZO906 2.9 30.0 1.0
CD2 A:HIS474 3.0 17.9 1.0
CE1 A:HIS474 3.1 17.6 1.0
CE1 A:HIS315 3.1 24.7 1.0
C28 A:6ZO906 3.1 27.7 1.0
CD2 A:HIS315 3.1 22.5 1.0
O32 A:6ZO906 3.2 27.3 1.0
C27 A:6ZO906 3.7 28.2 1.0
O29 A:6ZO906 4.1 29.4 1.0
CB A:ASP311 4.1 20.7 1.0
CG A:HIS474 4.1 16.1 1.0
ND1 A:HIS474 4.2 18.3 1.0
C26 A:6ZO906 4.2 30.4 1.0
ND1 A:HIS315 4.2 24.1 1.0
CG A:HIS315 4.2 22.9 1.0
OG1 A:THR209 4.3 29.4 1.0
CA A:CA901 4.3 52.2 1.0
CE1 A:HIS359 4.3 20.8 1.0
NE2 A:HIS359 4.6 19.2 1.0
CE A:MET361 4.6 21.6 1.0
O A:HOH1011 4.7 37.5 1.0
OD1 A:ASP171 4.7 28.3 1.0
O A:ASP311 4.9 19.9 1.0
CA A:ASP311 5.0 20.6 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 28 04:29:04 2024

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