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Calcium 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:

Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium 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 Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g65

Go back to Calcium Binding Sites List in 7g65
Calcium 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 Calcium with other atoms in the Ca 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:Ca901

b:35.6
occ:1.00
 OD1 A:ASP171 1.7 24.2 1.0
OG1 A:THR209 2.0 20.1 1.0
NE2 A:HIS359 2.1 16.1 1.0
OD2 A:ASP358 2.3 19.9 1.0
CG A:ASP171 2.8 24.5 1.0
CB A:THR209 2.9 18.9 1.0
CE1 A:HIS359 2.9 15.8 1.0
CD2 A:HIS359 3.0 15.4 1.0
CG2 A:THR209 3.1 19.1 1.0
CG A:ASP358 3.1 17.4 1.0
OD2 A:ASP171 3.3 33.5 1.0
OD1 A:ASP358 3.3 16.1 1.0
CA A:THR209 3.3 16.3 1.0
O A:HOH1012 3.8 33.9 1.0
N A:THR209 4.0 14.7 1.0
CB A:ASP171 4.0 20.1 1.0
ND1 A:HIS359 4.0 15.9 1.0
OD2 A:ASP311 4.0 17.6 1.0
N A:GLY172 4.1 16.6 1.0
CG A:HIS359 4.1 15.4 1.0
O3 A:SO4905 4.1 41.3 1.0
CA A:ASP171 4.2 18.5 1.0
O1 A:SO4905 4.3 40.9 1.0
CE1 A:HIS474 4.3 16.1 1.0
CB A:ASP358 4.4 16.4 1.0
CG A:ASP311 4.4 17.3 1.0
ZN A:ZN907 4.5 19.5 1.0
C A:ASP171 4.5 18.1 1.0
NE2 A:HIS474 4.6 16.6 1.0
C A:THR209 4.6 16.7 1.0
S A:SO4905 4.8 55.9 1.0
C A:LYS208 4.8 15.5 1.0
CB A:ASP311 4.8 16.6 1.0
CA A:GLY172 4.9 16.9 1.0
OD1 A:ASP311 4.9 18.9 1.0
O A:THR209 5.0 15.5 1.0

Calcium binding site 2 out of 2 in 7g65

Go back to Calcium Binding Sites List in 7g65
Calcium 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 Calcium with other atoms in the Ca 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:Ca909

b:16.0
occ:1.00
 O A:LEU745 2.2 15.3 1.0
OD1 A:ASP747 2.3 16.4 1.0
OD1 A:ASP739 2.3 14.3 1.0
OD1 A:ASP743 2.3 17.6 1.0
O A:HOH1399 2.3 19.6 1.0
OD1 A:ASN741 2.3 17.9 1.0
CG A:ASP743 3.3 19.1 1.0
CG A:ASN741 3.4 19.2 1.0
C A:LEU745 3.4 15.2 1.0
CG A:ASP739 3.5 14.7 1.0
CG A:ASP747 3.5 16.1 1.0
OD2 A:ASP743 3.8 19.8 1.0
ND2 A:ASN741 3.8 21.3 1.0
N A:ASP747 3.9 14.0 1.0
CA A:ASP739 4.0 14.0 1.0
C A:ARG746 4.0 15.8 1.0
N A:LEU745 4.0 14.5 1.0
CA A:ASP747 4.1 15.6 1.0
CA A:LEU745 4.2 14.9 1.0
O A:ARG746 4.2 15.5 1.0
CB A:ASP739 4.2 14.6 1.0
N A:ASP743 4.3 15.6 1.0
OD2 A:ASP739 4.4 14.4 1.0
OD2 A:ASP747 4.4 17.2 1.0
CB A:ASP747 4.4 14.6 1.0
N A:ARG746 4.4 15.1 1.0
CB A:LEU745 4.5 15.9 1.0
O A:PHE738 4.5 14.8 1.0
C A:ASP739 4.5 14.7 1.0
N A:ASN741 4.5 16.5 1.0
CB A:ASP743 4.5 17.9 1.0
O A:HOH1369 4.7 32.0 1.0
OE2 A:GLU751 4.7 26.9 1.0
CA A:ARG746 4.7 14.7 1.0
N A:TYR740 4.7 14.7 1.0
CB A:ASN741 4.7 16.9 1.0
N A:TYR742 4.8 16.2 1.0
CA A:ASP743 4.8 16.1 1.0
N A:GLY744 4.9 15.4 1.0
C A:ASN741 4.9 16.7 1.0
CA A:ASN741 4.9 17.0 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 22:32:11 2025

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