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Sodium in PDB 7g65: Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide, PDB code: 7g65 was solved by M.Stihle, J.Benz, D.Hunziker, K.Hada, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 45.81 / 1.73
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.777, 91.623, 118.712, 90, 90, 90
R / Rfree (%) 18.5 / 21.7

Other elements in 7g65:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide also contains other interesting chemical elements:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Fluorine (F) 3 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide (pdb code 7g65). 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 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide, PDB code: 7g65:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g65

Go back to Sodium Binding Sites List in 7g65
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide


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 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na908

b:24.1
occ:1.00
 O A:HOH1413 2.3 31.8 1.0
OG A:SER807 2.3 20.1 1.0
O A:HOH1264 2.4 27.1 1.0
O A:SER804 2.4 21.0 1.0
O A:HOH1364 2.4 31.5 1.0
O A:ASN801 2.5 19.2 1.0
C A:ASN801 3.4 19.1 1.0
CB A:SER807 3.5 22.0 1.0
C A:SER804 3.5 20.6 1.0
CA A:ASP802 3.8 21.8 1.0
N A:ASP802 3.9 20.2 1.0
N A:SER807 4.1 24.3 1.0
C A:ASP802 4.2 21.1 1.0
O A:HOH1053 4.2 36.4 1.0
O A:ASP802 4.2 18.7 1.0
CA A:CYS805 4.3 24.4 1.0
N A:CYS805 4.3 21.5 1.0
CA A:SER807 4.3 25.0 1.0
CB A:ASN801 4.3 18.1 1.0
N A:SER804 4.3 17.8 1.0
C A:CYS805 4.4 24.4 1.0
CA A:SER804 4.4 19.8 1.0
CA A:ASN801 4.4 18.6 1.0
O A:CYS805 4.5 24.1 1.0
O A:HOH1098 4.6 31.7 1.0
O A:HOH1271 4.6 32.2 1.0
OD1 A:ASP802 4.7 28.2 1.0
CB A:SER804 4.7 20.4 1.0
N A:ASN806 4.9 23.6 1.0
N A:GLU803 5.0 18.0 1.0

Sodium binding site 2 out of 2 in 7g65

Go back to Sodium Binding Sites List in 7g65
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide


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 4-Pyrrolidin-1-Yl- 3-[(E)-2-[4-(Trifluoromethoxy)Phenyl]Ethenyl]Benzamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na910

b:29.7
occ:1.00
 O A:TYR669 2.3 27.9 1.0
O A:MET675 2.3 23.6 1.0
O A:HOH1400 2.4 31.6 1.0
O A:ASP672 2.4 24.6 1.0
O A:HOH1436 2.7 40.1 1.0
C A:TYR669 3.4 28.3 1.0
C A:MET675 3.5 23.8 1.0
C A:ASP672 3.6 27.6 1.0
N A:MET675 4.1 25.9 1.0
CA A:TYR669 4.2 24.9 1.0
O A:LYS670 4.3 34.1 1.0
CA A:MET675 4.3 23.5 1.0
N A:SER676 4.4 20.6 1.0
O A:HOH1460 4.4 38.8 1.0
N A:LYS670 4.4 29.5 1.0
CA A:LYS673 4.4 30.9 1.0
N A:LYS673 4.4 26.2 1.0
CA A:SER676 4.4 20.6 1.0
CA A:ASP672 4.5 27.5 1.0
C A:LYS673 4.5 30.9 1.0
CB A:TYR669 4.5 23.3 1.0
N A:ASP672 4.5 30.3 1.0
C A:LYS670 4.6 32.2 1.0
CA A:LYS670 4.6 33.1 1.0
O A:LYS673 4.7 30.1 1.0
CB A:ASP672 4.7 25.8 1.0
CB A:MET675 5.0 22.2 1.0
N A:GLN674 5.0 28.9 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 23:25:46 2025

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