Atomistry » Calcium » PDB 7g2r-7g3u » 7g3d
Atomistry »
  Calcium »
    PDB 7g2r-7g3u »
      7g3d »

Calcium in PDB 7g3d: Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d was solved by M.Stihle, J.Benz, D.Hunziker, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 1.88
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.23, 91.79, 119.85, 90, 90, 90
R / Rfree (%) 17.7 / 21.8

Other elements in 7g3d:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm (pdb code 7g3d). 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm, PDB code: 7g3d:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g3d

Go back to Calcium Binding Sites List in 7g3d
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca907

b:30.3
occ:1.00
 OD1 A:ASP171 2.0 28.6 1.0
OG1 A:THR209 2.0 23.3 1.0
NE2 A:HIS359 2.2 22.1 1.0
OD2 A:ASP358 2.2 24.9 1.0
CG A:ASP171 2.7 27.8 1.0
OD2 A:ASP171 2.8 37.0 1.0
CB A:THR209 3.0 23.2 1.0
CG A:ASP358 3.0 22.1 1.0
CE1 A:HIS359 3.1 21.5 1.0
CD2 A:HIS359 3.2 21.2 1.0
CG2 A:THR209 3.3 24.3 1.0
OD1 A:ASP358 3.3 21.7 1.0
O1 A:SO4903 3.4 76.6 1.0
CA A:THR209 3.4 22.1 1.0
O A:HOH1014 3.6 43.4 1.0
N A:THR209 3.9 21.9 1.0
CB A:ASP171 4.0 25.4 1.0
ND1 A:HIS359 4.1 21.0 1.0
OD1 A:ASP311 4.2 24.0 1.0
CG A:HIS359 4.2 19.9 1.0
N A:GLY172 4.2 21.9 1.0
CA A:ASP171 4.3 22.8 1.0
O A:HOH1002 4.4 33.4 1.0
CB A:ASP358 4.4 20.9 1.0
CE1 A:HIS474 4.4 21.9 1.0
CG A:ASP311 4.5 22.9 1.0
ZN A:ZN909 4.6 27.4 1.0
NE2 A:HIS474 4.6 21.9 1.0
C A:ASP171 4.7 22.1 1.0
C A:THR209 4.7 22.1 1.0
C A:LYS208 4.7 22.9 1.0
S A:SO4903 4.8 80.0 1.0
CB A:ASP311 4.8 22.7 1.0
OD2 A:ASP311 4.9 24.9 1.0

Calcium binding site 2 out of 2 in 7g3d

Go back to Calcium Binding Sites List in 7g3d
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 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 4-Tert-Butyl-2- Chloro-5-(1H-Pyrazolo[3,4-B]Pyridin-3-Ylmethoxy)Benzonitrile, I.E. Smiles Cc(C)(C)C1CC(Cl)C(C#N)CC1OCC1=NNC2NCCCC12 with IC50=0.0201187 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca911

b:21.6
occ:1.00
 OD1 A:ASP739 2.3 19.9 1.0
OD1 A:ASP747 2.3 20.6 1.0
OD1 A:ASP743 2.3 25.8 1.0
OD1 A:ASN741 2.3 23.5 1.0
O A:LEU745 2.3 19.5 1.0
O A:HOH1374 2.3 24.9 1.0
CG A:ASP743 3.3 23.6 1.0
CG A:ASN741 3.4 26.4 1.0
CG A:ASP739 3.5 21.4 1.0
C A:LEU745 3.5 21.1 1.0
CG A:ASP747 3.5 22.0 1.0
OD2 A:ASP743 3.7 26.6 1.0
ND2 A:ASN741 3.8 28.6 1.0
CA A:ASP739 3.9 19.7 1.0
N A:ASP747 4.0 19.7 1.0
N A:LEU745 4.1 20.1 1.0
C A:ARG746 4.1 20.1 1.0
O A:ARG746 4.2 20.4 1.0
CB A:ASP739 4.2 19.9 1.0
CA A:LEU745 4.2 20.5 1.0
CA A:ASP747 4.2 20.1 1.0
N A:ASP743 4.3 21.9 1.0
OD2 A:ASP747 4.4 23.7 1.0
OD2 A:ASP739 4.4 21.9 1.0
N A:ASN741 4.4 21.5 1.0
CB A:LEU745 4.5 23.6 1.0
O A:PHE738 4.5 18.1 1.0
C A:ASP739 4.5 20.5 1.0
CB A:ASP747 4.5 20.1 1.0
N A:ARG746 4.5 21.2 1.0
CB A:ASP743 4.5 21.9 1.0
OE2 A:GLU751 4.7 33.0 1.0
CB A:ASN741 4.7 23.0 1.0
N A:TYR740 4.7 22.1 1.0
N A:TYR742 4.8 22.5 1.0
CA A:ARG746 4.8 22.0 1.0
CA A:ASP743 4.8 21.2 1.0
O A:HOH1365 4.8 43.2 1.0
C A:ASN741 4.9 23.3 1.0
N A:GLY744 4.9 20.7 1.0
CA A:ASN741 4.9 23.1 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 15:37:03 2025

Last articles

Na in 7G58
Na in 7G53
Na in 7G51
Na in 7G5C
Na in 7G4Q
Na in 7G4Z
Na in 7G55
Na in 7G4S
Na in 7G4X
Na in 7G52
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy