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Sodium 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
Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium 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 Sodium atom.
In total 2 binding sites of Sodium where 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:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g5e

Go back to Sodium Binding Sites List in 7g5e
Sodium binding site 1 out of 2 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 Sodium with other atoms in the Na 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:Na904

b:33.5
occ:1.00
 OG A:SER807 2.3 23.5 1.0
O A:HOH1352 2.3 25.7 1.0
O A:SER804 2.4 23.2 1.0
O A:HOH1093 2.5 26.2 1.0
O A:HOH1372 2.6 28.0 1.0
O A:ASN801 2.7 25.0 1.0
C A:SER804 3.5 25.8 1.0
CB A:SER807 3.5 24.7 1.0
C A:ASN801 3.5 26.8 1.0
CA A:ASP802 4.0 25.6 1.0
N A:SER807 4.0 27.1 1.0
N A:ASP802 4.2 24.9 1.0
CA A:CYS805 4.2 30.5 1.0
N A:CYS805 4.2 25.6 1.0
O A:ASP802 4.2 24.1 1.0
CA A:SER807 4.2 27.6 1.0
C A:CYS805 4.3 31.0 1.0
O A:CYS805 4.3 30.5 1.0
C A:ASP802 4.3 25.7 1.0
CA A:SER804 4.4 21.7 1.0
CB A:ASN801 4.4 24.2 1.0
N A:SER804 4.5 24.4 1.0
O A:HOH1152 4.5 33.4 1.0
CA A:ASN801 4.5 25.0 1.0
O A:HOH1202 4.6 30.6 1.0
OD1 A:ASP802 4.7 36.1 1.0
CB A:SER804 4.8 22.9 1.0
N A:ASN806 4.9 29.9 1.0
C A:SER807 4.9 30.5 1.0
N A:SER808 5.0 35.2 1.0

Sodium binding site 2 out of 2 in 7g5e

Go back to Sodium Binding Sites List in 7g5e
Sodium binding site 2 out of 2 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 Sodium with other atoms in the Na binding site number 2 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:Na906

b:36.3
occ:1.00
 O A:HOH1214 2.3 42.7 1.0
O A:TYR669 2.3 35.7 1.0
O A:MET675 2.4 30.0 1.0
O A:ASP672 2.4 29.6 1.0
O A:HOH1376 3.4 46.0 1.0
C A:TYR669 3.5 33.0 1.0
C A:MET675 3.6 29.9 1.0
C A:ASP672 3.6 30.5 1.0
O A:LYS670 4.2 34.7 1.0
N A:MET675 4.3 29.7 1.0
CA A:TYR669 4.3 32.4 1.0
N A:SER676 4.4 25.9 1.0
CA A:LYS673 4.4 31.6 1.0
CA A:SER676 4.4 27.1 1.0
CA A:MET675 4.5 27.1 1.0
N A:LYS673 4.5 29.7 1.0
N A:LYS670 4.5 34.4 1.0
CA A:ASP672 4.5 29.3 1.0
C A:LYS670 4.6 34.7 1.0
CA A:LYS670 4.6 36.6 1.0
C A:LYS673 4.6 32.1 1.0
CB A:TYR669 4.6 30.8 1.0
N A:ASP672 4.6 33.3 1.0
CB A:ASP672 4.8 30.6 1.0
O A:LYS673 4.9 29.1 1.0
N A:GLN674 5.0 30.1 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 23:22:55 2025

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