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Calcium in PDB 8c3o: Crystal Structure of Autotaxin Gamma and Compound Mey-003

Enzymatic activity of Crystal Structure of Autotaxin Gamma and Compound Mey-003

All present enzymatic activity of Crystal Structure of Autotaxin Gamma and Compound Mey-003:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Autotaxin Gamma and Compound Mey-003, PDB code: 8c3o was solved by M.C.Eymery, A.A.Mccarthy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 57.64 / 2.47
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 53.925, 288.478, 57.643, 90, 90.12, 90
R / Rfree (%) 21.4 / 27.1

Other elements in 8c3o:

The structure of Crystal Structure of Autotaxin Gamma and Compound Mey-003 also contains other interesting chemical elements:

Iodine (I) 37 atoms
Zinc (Zn) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Autotaxin Gamma and Compound Mey-003 (pdb code 8c3o). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Autotaxin Gamma and Compound Mey-003, PDB code: 8c3o:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 8c3o

Go back to Calcium Binding Sites List in 8c3o
Calcium binding site 1 out of 2 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Autotaxin Gamma and Compound Mey-003 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca930

b:15.4
occ:1.00
OD1 A:ASP773 2.1 21.4 1.0
OD1 A:ASP769 2.2 24.0 1.0
OD1 A:ASP767 2.3 20.8 1.0
OD1 A:ASP765 2.5 15.8 1.0
O A:HOH1007 2.5 19.6 1.0
O A:LEU771 2.5 15.9 1.0
CG A:ASP773 3.2 23.9 1.0
CG A:ASP769 3.3 18.4 1.0
CG A:ASP767 3.4 19.6 1.0
C A:LEU771 3.5 17.2 1.0
CG A:ASP765 3.7 15.2 1.0
N A:LEU771 3.7 18.9 1.0
OD2 A:ASP773 3.7 20.9 1.0
OD2 A:ASP767 3.9 23.6 1.0
OD2 A:ASP769 3.9 20.9 1.0
N A:ASP769 4.0 16.0 1.0
CA A:LEU771 4.0 18.2 1.0
CA A:ASP765 4.1 18.4 1.0
CB A:LEU771 4.3 18.6 1.0
CB A:ASP769 4.3 15.6 1.0
N A:ASP773 4.4 22.2 1.0
CB A:ASP765 4.4 14.3 1.0
N A:GLY770 4.4 15.2 1.0
CB A:ASP773 4.4 19.0 1.0
CA A:ASP769 4.5 19.1 1.0
N A:ASP767 4.5 18.4 1.0
CA A:ASP773 4.6 22.0 1.0
C A:HIS772 4.6 22.6 1.0
OD2 A:ASP765 4.6 21.7 1.0
N A:TYR768 4.6 19.6 1.0
C A:ASP765 4.6 17.4 1.0
C A:ASP769 4.6 16.6 1.0
N A:HIS772 4.6 19.9 1.0
C A:ASP767 4.6 16.6 1.0
O A:PHE764 4.7 17.7 1.0
CB A:ASP767 4.7 14.7 1.0
N A:TYR766 4.8 16.0 1.0
C A:GLY770 4.8 19.1 1.0
CA A:ASP767 4.9 15.5 1.0
O A:HIS772 4.9 24.8 1.0

Calcium binding site 2 out of 2 in 8c3o

Go back to Calcium Binding Sites List in 8c3o
Calcium binding site 2 out of 2 in the Crystal Structure of Autotaxin Gamma and Compound Mey-003


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Autotaxin Gamma and Compound Mey-003 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca922

b:16.6
occ:1.00
OD1 B:ASP769 2.3 22.6 1.0
OD1 B:ASP773 2.3 21.3 1.0
OD1 B:ASP767 2.3 20.9 1.0
OD1 B:ASP765 2.5 19.6 1.0
O B:LEU771 2.6 15.8 1.0
CG B:ASP769 3.3 17.1 1.0
CG B:ASP767 3.3 19.0 1.0
C B:LEU771 3.5 18.6 1.0
CG B:ASP773 3.5 20.1 1.0
OD2 B:ASP767 3.6 21.9 1.0
CG B:ASP765 3.7 16.4 1.0
OD2 B:ASP769 3.7 20.2 1.0
N B:LEU771 3.9 17.4 1.0
CA B:ASP765 4.0 17.9 1.0
CA B:LEU771 4.1 16.6 1.0
N B:ASP773 4.2 21.0 1.0
N B:ASP769 4.2 14.2 1.0
OD2 B:ASP773 4.3 24.3 1.0
CB B:LEU771 4.3 14.5 1.0
CB B:ASP765 4.3 14.7 1.0
CA B:ASP773 4.4 20.3 1.0
C B:HIS772 4.4 21.1 1.0
CB B:ASP769 4.5 16.6 1.0
CB B:ASP773 4.6 17.4 1.0
N B:HIS772 4.6 22.2 1.0
N B:ASP767 4.6 15.6 1.0
C B:ASP765 4.6 20.4 1.0
N B:TYR768 4.6 18.2 1.0
OD2 B:ASP765 4.6 17.3 1.0
O B:PHE764 4.6 20.4 1.0
O B:HIS772 4.6 23.4 1.0
CB B:ASP767 4.7 14.7 1.0
N B:GLY770 4.7 15.7 1.0
CA B:ASP769 4.7 14.9 1.0
N B:TYR766 4.8 21.0 1.0
C B:ASP767 4.8 18.9 1.0
C B:ASP769 4.8 15.6 1.0
CA B:ASP767 4.9 15.4 1.0
CA B:HIS772 4.9 16.6 1.0

Reference:

M.C.Eymery, K.A.Nguyen, S.Basu, J.Hausmann, V.K.T.Nguyen, H.P.Seidel, L.Gutierrez, A.Boumendjel, A.A.Mccarthy. Discovery of Potent Chromone-Based Autotaxin Inhibitors Inspired By Cannabinoids Eur.J.Med.Chem. 2023.
ISSN: ISSN 0223-5234
DOI: 10.1016/J.EJMECH.2023.115944
Page generated: Thu Dec 28 01:35:58 2023

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