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Calcium in PDB 7g3f: Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm, PDB code: 7g3f was solved by M.Stihle, J.Benz, D.Hunziker, L.Green, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.28 / 1.85
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.473, 91.165, 118.586, 90, 90, 90
R / Rfree (%) 18 / 22.4

Other elements in 7g3f:

The structure of Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm also contains other interesting chemical elements:

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

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm (pdb code 7g3f). 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 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm, PDB code: 7g3f:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3f

Go back to Calcium Binding Sites List in 7g3f
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 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 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:23.2
occ:1.00
 OD1 A:ASP171 1.9 21.4 1.0
OG1 A:THR209 1.9 18.2 1.0
NE2 A:HIS359 2.1 16.4 1.0
OD2 A:ASP358 2.2 25.5 1.0
O A:ACT904 2.4 43.8 1.0
CG A:ASP171 2.7 21.8 1.0
OD2 A:ASP171 2.9 31.1 1.0
CE1 A:HIS359 3.0 16.2 1.0
CB A:THR209 3.0 19.6 1.0
CD2 A:HIS359 3.1 16.6 1.0
CG A:ASP358 3.1 22.1 1.0
CG2 A:THR209 3.4 20.0 1.0
OD1 A:ASP358 3.5 18.4 1.0
CA A:THR209 3.5 19.6 1.0
C A:ACT904 3.5 42.2 1.0
N A:THR209 3.9 19.5 1.0
OD1 A:ASP311 4.0 19.6 1.0
CB A:ASP171 4.0 19.6 1.0
ND1 A:HIS359 4.1 16.1 1.0
CH3 A:ACT904 4.1 40.3 1.0
O A:HOH1003 4.1 22.8 1.0
CG A:HIS359 4.1 15.6 1.0
CE1 A:HIS474 4.3 17.5 1.0
CG A:ASP311 4.3 18.8 1.0
N A:GLY172 4.3 19.9 1.0
CA A:ASP171 4.4 18.8 1.0
ZN A:ZN906 4.4 20.5 1.0
CB A:ASP358 4.4 18.9 1.0
OXT A:ACT904 4.4 31.1 1.0
NE2 A:HIS474 4.5 15.8 1.0
OD2 A:ASP311 4.7 20.1 1.0
C A:LYS208 4.7 19.6 1.0
CB A:ASP311 4.7 18.0 1.0
C A:ASP171 4.8 19.5 1.0
C A:THR209 4.9 19.5 1.0

Calcium binding site 2 out of 2 in 7g3f

Go back to Calcium Binding Sites List in 7g3f
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 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 2-[(2-Tert-Butyl-5- Chloro-4-Cyanophenoxy)Methyl]-3-Methylimidazole-4-Carbonitrile, I.E. Smiles C1C(C(Cc(C1C(C)(C)C)OCC1=Nc=C(N1C)C#N)Cl)C#N with IC50=0.0496453 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca908

b:15.0
occ:1.00
 OD1 A:ASP747 2.2 19.4 1.0
OD1 A:ASN741 2.3 17.6 1.0
OD1 A:ASP739 2.3 13.4 1.0
OD1 A:ASP743 2.3 18.0 1.0
O A:HOH1357 2.3 23.3 1.0
O A:LEU745 2.3 16.8 1.0
CG A:ASP743 3.3 18.9 1.0
CG A:ASN741 3.4 19.1 1.0
CG A:ASP739 3.5 13.3 1.0
C A:LEU745 3.5 17.0 1.0
CG A:ASP747 3.5 19.4 1.0
OD2 A:ASP743 3.8 19.0 1.0
ND2 A:ASN741 3.9 21.9 1.0
CA A:ASP739 3.9 15.1 1.0
N A:ASP747 3.9 17.0 1.0
N A:LEU745 4.1 17.1 1.0
C A:ARG746 4.1 16.9 1.0
CB A:ASP739 4.2 14.2 1.0
CA A:ASP747 4.2 17.5 1.0
CA A:LEU745 4.2 15.9 1.0
O A:ARG746 4.3 14.3 1.0
OD2 A:ASP747 4.3 19.4 1.0
N A:ASN741 4.4 16.4 1.0
N A:ASP743 4.4 17.5 1.0
OD2 A:ASP739 4.4 12.9 1.0
C A:ASP739 4.4 16.3 1.0
CB A:ASP747 4.5 18.9 1.0
N A:ARG746 4.5 17.1 1.0
O A:PHE738 4.5 16.5 1.0
CB A:LEU745 4.5 17.9 1.0
CB A:ASP743 4.5 18.0 1.0
CB A:ASN741 4.7 18.4 1.0
N A:TYR740 4.7 15.7 1.0
N A:TYR742 4.7 15.8 1.0
CA A:ARG746 4.7 17.5 1.0
OE2 A:GLU751 4.8 27.7 1.0
N A:GLY744 4.8 16.8 1.0
CA A:ASN741 4.8 16.3 1.0
C A:ASN741 4.9 17.9 1.0
CA A:ASP743 4.9 17.3 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 15:37:02 2025

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