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Calcium 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:

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

Calcium Binding Sites:

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

Calcium binding site 1 out of 1 in 7g5e

Go back to Calcium Binding Sites List in 7g5e
Calcium 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 Calcium with other atoms in the Ca 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:Ca905

b:18.5
occ:1.00
 OD1 A:ASN741 2.2 21.9 1.0
O A:LEU745 2.2 18.6 1.0
OD1 A:ASP747 2.2 19.8 1.0
OD1 A:ASP739 2.3 15.3 1.0
O A:HOH1338 2.3 22.4 1.0
OD1 A:ASP743 2.4 19.6 1.0
CG A:ASN741 3.3 22.9 1.0
CG A:ASP743 3.3 20.8 1.0
C A:LEU745 3.4 18.5 1.0
CG A:ASP739 3.5 17.9 1.0
CG A:ASP747 3.5 20.4 1.0
OD2 A:ASP743 3.7 20.1 1.0
ND2 A:ASN741 3.7 24.0 1.0
CA A:ASP739 3.9 19.2 1.0
N A:ASP747 3.9 19.6 1.0
N A:LEU745 4.1 17.7 1.0
C A:ARG746 4.1 20.7 1.0
CA A:ASP747 4.1 20.0 1.0
O A:ARG746 4.2 20.8 1.0
CA A:LEU745 4.2 18.4 1.0
CB A:ASP739 4.2 16.7 1.0
OD2 A:ASP747 4.3 22.6 1.0
N A:ASP743 4.3 22.4 1.0
OD2 A:ASP739 4.4 17.2 1.0
O A:PHE738 4.4 18.2 1.0
N A:ASN741 4.4 20.3 1.0
CB A:ASP747 4.4 19.6 1.0
C A:ASP739 4.4 19.6 1.0
CB A:LEU745 4.4 18.1 1.0
N A:ARG746 4.5 17.8 1.0
CB A:ASP743 4.6 19.4 1.0
CB A:ASN741 4.6 20.4 1.0
N A:TYR742 4.7 23.3 1.0
OE2 A:GLU751 4.7 27.2 1.0
N A:TYR740 4.7 20.1 1.0
O A:HOH1267 4.8 31.1 1.0
CA A:ARG746 4.8 20.7 1.0
CA A:ASN741 4.8 22.8 1.0
C A:ASN741 4.8 22.2 1.0
N A:GLY744 4.8 20.7 1.0
CA A:ASP743 4.8 20.7 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: Wed Jul 9 22:29:04 2025

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