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Calcium in PDB 7g3g: Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm, PDB code: 7g3g was solved by M.Stihle, J.Benz, D.Hunziker, H.Ratni, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.31 / 1.87
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.728, 91.178, 118.716, 90, 90, 90
R / Rfree (%) 16.9 / 20.4

Other elements in 7g3g:

The structure of Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm (pdb code 7g3g). 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 Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm, PDB code: 7g3g:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3g

Go back to Calcium Binding Sites List in 7g3g
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm


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 Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:27.7
occ:1.00
 OG1 A:THR209 2.0 20.1 1.0
OD1 A:ASP171 2.0 26.2 1.0
NE2 A:HIS359 2.2 22.2 1.0
OD2 A:ASP358 2.3 25.6 1.0
O A:ACT904 2.5 53.8 1.0
CG A:ASP171 2.7 27.6 1.0
OD2 A:ASP171 2.8 33.8 1.0
CB A:THR209 3.0 23.5 1.0
CE1 A:HIS359 3.1 21.8 1.0
CG A:ASP358 3.1 23.9 1.0
CD2 A:HIS359 3.1 23.1 1.0
CG2 A:THR209 3.3 23.4 1.0
OD1 A:ASP358 3.4 21.4 1.0
CA A:THR209 3.5 22.6 1.0
C A:ACT904 3.6 52.2 1.0
N A:THR209 4.0 22.0 1.0
CB A:ASP171 4.1 25.8 1.0
CH3 A:ACT904 4.1 50.6 1.0
OD1 A:ASP311 4.1 24.4 1.0
ND1 A:HIS359 4.2 22.1 1.0
CG A:HIS359 4.2 22.9 1.0
O A:HOH1001 4.2 31.2 1.0
N A:GLY172 4.3 21.8 1.0
CE1 A:HIS474 4.3 20.6 1.0
CA A:ASP171 4.4 24.5 1.0
CB A:ASP358 4.4 21.4 1.0
CG A:ASP311 4.4 27.1 1.0
ZN A:ZN907 4.5 25.6 1.0
OXT A:ACT904 4.5 39.3 1.0
NE2 A:HIS474 4.5 20.9 1.0
C A:ASP171 4.7 24.0 1.0
C A:LYS208 4.8 23.7 1.0
C A:THR209 4.8 22.3 1.0
CB A:ASP311 4.8 24.7 1.0
OD2 A:ASP311 4.9 28.0 1.0
OH A:TYR306 5.0 26.7 1.0

Calcium binding site 2 out of 2 in 7g3g

Go back to Calcium Binding Sites List in 7g3g
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm


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 Rat Autotaxin in Complex with 5-Tert-Butyl-2- Methyl-4-[(2-Oxo-1H-Pyridin-3-Yl)Methoxy]Benzonitrile, I.E. Smiles N#CC1CC(C(C)(C)C)C(OCC2=Cc=CNC2=O)CC1C with IC50=0.0896883 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca909

b:20.5
occ:1.00
 OD1 A:ASP747 2.2 22.9 1.0
OD1 A:ASN741 2.3 22.3 1.0
O A:LEU745 2.3 19.3 1.0
OD1 A:ASP739 2.3 19.2 1.0
OD1 A:ASP743 2.3 24.1 1.0
O A:HOH1346 2.3 24.3 1.0
CG A:ASP743 3.3 24.6 1.0
CG A:ASN741 3.3 23.8 1.0
CG A:ASP747 3.5 23.4 1.0
C A:LEU745 3.5 20.6 1.0
CG A:ASP739 3.5 19.7 1.0
OD2 A:ASP743 3.6 24.0 1.0
ND2 A:ASN741 3.8 26.9 1.0
N A:ASP747 3.9 19.9 1.0
CA A:ASP739 4.0 20.6 1.0
N A:LEU745 4.0 19.5 1.0
C A:ARG746 4.1 22.4 1.0
CA A:ASP747 4.2 21.9 1.0
CA A:LEU745 4.2 20.2 1.0
O A:ARG746 4.3 21.2 1.0
CB A:ASP739 4.3 20.0 1.0
OD2 A:ASP747 4.3 26.1 1.0
N A:ASP743 4.3 23.3 1.0
OD2 A:ASP739 4.4 19.1 1.0
CB A:ASP747 4.4 22.8 1.0
N A:ASN741 4.5 21.5 1.0
O A:PHE738 4.5 19.0 1.0
CB A:LEU745 4.5 22.0 1.0
C A:ASP739 4.5 21.4 1.0
N A:ARG746 4.5 20.0 1.0
CB A:ASP743 4.5 23.0 1.0
CB A:ASN741 4.6 22.7 1.0
N A:TYR740 4.7 21.1 1.0
N A:TYR742 4.8 22.4 1.0
OE2 A:GLU751 4.8 39.6 1.0
CA A:ARG746 4.8 21.4 1.0
N A:GLY744 4.8 21.1 1.0
CA A:ASP743 4.8 21.8 1.0
CA A:ASN741 4.9 22.2 1.0
C A:ASN741 4.9 23.5 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: Sat Feb 8 15:36:58 2025

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