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Zinc in PDB 7g49: Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One, PDB code: 7g49 was solved by M.Stihle, J.Benz, D.Hunziker, E.Goetschi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.899, 92.064, 119.722, 90, 90, 90
R / Rfree (%) 16 / 20.8

Other elements in 7g49:

The structure of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One (pdb code 7g49). 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 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One, PDB code: 7g49:

Zinc binding site 1 out of 1 in 7g49

Go back to Zinc Binding Sites List in 7g49
Zinc binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One


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 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:21.2
occ:1.00
 NE2 A:HIS315 2.0 22.1 1.0
OD2 A:ASP311 2.0 18.8 1.0
NE2 A:HIS474 2.0 19.1 1.0
O A:HOH1493 2.0 29.3 1.0
OD1 A:ASP311 2.4 18.7 1.0
CG A:ASP311 2.6 18.6 1.0
CD2 A:HIS315 3.0 21.1 1.0
CD2 A:HIS474 3.0 20.2 1.0
CE1 A:HIS315 3.0 24.9 1.0
CE1 A:HIS474 3.0 20.3 1.0
HD2 A:HIS315 3.1 25.3 1.0
HD2 A:HIS474 3.1 24.2 1.0
HE1 A:HIS315 3.2 29.8 1.0
HE1 A:HIS474 3.3 24.3 1.0
HE1 A:HIS359 3.5 23.7 1.0
O A:HOH1046 3.5 39.4 1.0
HE1 A:MET361 3.5 20.3 1.0
HG1 A:THR209 3.9 28.9 1.0
CB A:ASP311 4.1 19.4 1.0
ND1 A:HIS315 4.1 22.8 1.0
CG A:HIS315 4.1 16.8 1.0
ND1 A:HIS474 4.1 18.9 1.0
CG A:HIS474 4.1 17.0 1.0
CE1 A:HIS359 4.2 19.8 1.0
HE2 A:HIS359 4.2 24.6 1.0
OG1 A:THR209 4.3 24.1 1.0
HB2 A:ASP311 4.4 23.3 1.0
CE A:MET361 4.4 16.9 1.0
OD2 A:ASP171 4.5 27.1 1.0
HE2 A:MET361 4.5 20.3 1.0
NE2 A:HIS359 4.5 20.5 1.0
HB3 A:ASP311 4.5 23.3 1.0
OD1 A:ASP171 4.9 25.2 1.0
O A:ASP311 4.9 17.3 1.0
HA A:ASP311 4.9 21.7 1.0
HD1 A:HIS315 4.9 27.3 1.0
HD1 A:HIS474 4.9 22.7 1.0
HE3 A:MET361 4.9 20.3 1.0
CA A:ASP311 5.0 18.1 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: Sun Feb 9 00:26:19 2025

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