Atomistry » Zinc » PDB 7g2k-7g3n » 7g3g
Atomistry »
  Zinc »
    PDB 7g2k-7g3n »
      7g3g »

Zinc 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:

Calcium (Ca) 2 atoms
Sodium (Na) 2 atoms
Chlorine (Cl) 1 atom

Zinc Binding Sites:

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

Zinc binding site 1 out of 1 in 7g3g

Go back to Zinc Binding Sites List in 7g3g
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn907

b:25.6
occ:1.00
 OXT A:ACT904 1.9 39.3 1.0
OD1 A:ASP311 2.0 24.4 1.0
NE2 A:HIS474 2.0 20.9 1.0
NE2 A:HIS315 2.1 26.1 1.0
O A:ACT904 2.4 53.8 1.0
C A:ACT904 2.5 52.2 1.0
CG A:ASP311 2.7 27.1 1.0
OD2 A:ASP311 2.7 28.0 1.0
CD2 A:HIS474 3.0 20.2 1.0
CD2 A:HIS315 3.0 24.6 1.0
CE1 A:HIS474 3.0 20.6 1.0
CE1 A:HIS315 3.1 26.9 1.0
CH3 A:ACT904 3.9 50.6 1.0
CB A:ASP311 4.1 24.7 1.0
ND1 A:HIS474 4.2 20.4 1.0
CG A:HIS474 4.2 19.4 1.0
CE1 A:HIS359 4.2 21.8 1.0
CG A:HIS315 4.2 27.6 1.0
ND1 A:HIS315 4.2 26.1 1.0
O A:HOH1001 4.3 31.2 1.0
NE2 A:HIS359 4.4 22.2 1.0
CA A:CA901 4.5 27.7 1.0
CE A:MET361 4.5 24.8 1.0
OD1 A:ASP171 4.6 26.2 1.0
OG1 A:THR209 4.6 20.1 1.0
O A:ASP311 4.8 23.2 1.0
O A:HOH1040 4.9 48.9 1.0
CA A:ASP311 5.0 24.6 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: Sun Feb 9 00:21:49 2025

Last articles

Mg in 8YSL
Mg in 8YSG
Mg in 8YSE
Mg in 8YSD
Mg in 8YSC
Mg in 8YS5
Mg in 8YRV
Mg in 8YQZ
Mg in 8YQY
Mg in 8YQW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy