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Zinc in PDB 7g5e: Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm, PDB code: 7g5e was solved by M.Stihle, J.Benz, D.Hunziker, M.Boehringer, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.22 / 1.96
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.7, 91.434, 117.975, 90, 90, 90
R / Rfree (%) 19.3 / 24.3

Other elements in 7g5e:

The structure of Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm also contains other interesting chemical elements:

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

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm (pdb code 7g5e). 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 Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm, PDB code: 7g5e:

Zinc binding site 1 out of 1 in 7g5e

Go back to Zinc Binding Sites List in 7g5e
Zinc binding site 1 out of 1 in the Crystal Structure of Rat Autotaxin in Complex with Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 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 Rac-(4S,6R,7S,8S, 11S,12S,15R,16R)-4,6-Dihydroxy-12,16-Dimethyl-15-[Rac-(2R)-6-Methyl- 5-Methylidene-4-Oxoheptan-2-Yl]Pentacyclo[9.7.0.01,3.03,8.012, 16]Octadecane-7-Carboxylic Acid, I.E. Smiles [C@@]123[C@@]4(C1) [C@H]([C@]1([C@](CC4)([C@H](CC1)[C@@H](Cc(=O)C(=C)C(C)C)C)C)C) Cc[C@H]2[C@@H]([C@@H](C[C@@H]3O)O)C(=O)O with IC50=0.0603796 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn903

b:25.8
occ:1.00
 NE2 A:HIS474 2.1 20.6 1.0
NE2 A:HIS315 2.1 23.2 1.0
OD1 A:ASP311 2.2 22.1 1.0
O A:HOH1375 2.2 38.6 1.0
OD2 A:ASP311 2.6 21.5 1.0
CG A:ASP311 2.7 22.1 1.0
CD2 A:HIS474 3.0 17.8 1.0
CD2 A:HIS315 3.0 21.0 1.0
CE1 A:HIS474 3.0 20.1 1.0
CE1 A:HIS315 3.1 21.7 1.0
O A:HOH1007 4.0 40.5 1.0
CE1 A:HIS359 4.1 18.9 1.0
ND1 A:HIS474 4.2 18.2 1.0
ND1 A:HIS315 4.2 22.4 1.0
CG A:HIS474 4.2 18.3 1.0
CG A:HIS315 4.2 21.3 1.0
OG1 A:THR209 4.2 29.7 1.0
CB A:ASP311 4.2 20.9 1.0
NE2 A:HIS359 4.4 20.3 1.0
CE A:MET361 4.5 19.5 1.0
OD1 A:ASP171 4.8 33.9 1.0
O A:ASP311 4.9 22.5 1.0
OD2 A:ASP171 4.9 32.2 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 00:30:45 2025

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