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Calcium in PDB 5s9n: Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%

Enzymatic activity of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%

All present enzymatic activity of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%, PDB code: 5s9n was solved by M.Stihle, D.Hunziker, J.Benz, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.90 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.114, 91.731, 120.21, 90, 90, 90
R / Rfree (%) 19.1 / 23.3

Other elements in 5s9n:

The structure of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% also contains other interesting chemical elements:

Chlorine (Cl) 4 atoms
Zinc (Zn) 1 atom
Sodium (Na) 1 atom
Fluorine (F) 3 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% (pdb code 5s9n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%, PDB code: 5s9n:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 5s9n

Go back to Calcium Binding Sites List in 5s9n
Calcium binding site 1 out of 2 in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca903

b:33.0
occ:1.00
 O A:ASP672 2.3 28.6 1.0
O A:TYR669 2.3 31.5 1.0
O A:MET675 2.3 25.5 1.0
O A:HOH1362 2.4 44.2 1.0
O A:HOH1178 2.4 33.7 1.0
O A:HOH1363 2.5 38.7 1.0
C A:MET675 3.4 26.8 1.0
C A:ASP672 3.4 29.8 1.0
C A:TYR669 3.5 31.2 1.0
N A:MET675 4.1 28.5 1.0
O A:HOH1384 4.2 44.7 1.0
N A:SER676 4.3 22.9 1.0
CA A:LYS673 4.3 33.1 1.0
N A:LYS673 4.3 30.9 1.0
O A:LYS670 4.3 42.8 1.0
CA A:TYR669 4.3 27.1 1.0
CA A:MET675 4.3 24.7 1.0
CA A:SER676 4.4 24.8 1.0
CA A:ASP672 4.4 31.2 1.0
C A:LYS673 4.4 33.4 1.0
N A:LYS670 4.4 32.5 1.0
N A:ASP672 4.6 36.0 1.0
C A:LYS670 4.6 34.0 1.0
CB A:ASP672 4.6 30.3 1.0
O A:LYS673 4.6 33.3 1.0
CA A:LYS670 4.6 35.7 1.0
CB A:TYR669 4.6 28.3 1.0
N A:GLN674 4.9 29.0 1.0
C A:GLN674 4.9 29.9 1.0
CB A:SER676 5.0 25.4 1.0

Calcium binding site 2 out of 2 in 5s9n

Go back to Calcium Binding Sites List in 5s9n
Calcium binding site 2 out of 2 in the Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3%


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Autotaxin, [4-(Trifluoromethoxy)Phenyl]Methyl (3AS,6AS)-2-(1H- Benzotriazole-5-Carbonyl)-1,3,3A,4,6,6A-Hexahydropyrrolo[3,4- C]Pyrrole-5-Carboxylate, 1.80A, P212121, Rfree=23.3% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca904

b:20.2
occ:1.00
 OD1 A:ASP747 2.2 19.1 1.0
O A:HOH1351 2.3 26.0 1.0
OD1 A:ASN741 2.3 21.7 1.0
OD1 A:ASP739 2.4 17.5 1.0
O A:LEU745 2.4 16.3 1.0
OD1 A:ASP743 2.4 22.0 1.0
CG A:ASP743 3.3 22.0 1.0
CG A:ASN741 3.4 28.5 1.0
CG A:ASP747 3.5 20.1 1.0
CG A:ASP739 3.5 17.8 1.0
C A:LEU745 3.5 22.5 1.0
OD2 A:ASP743 3.6 26.4 1.0
ND2 A:ASN741 3.8 27.2 1.0
CA A:ASP739 3.9 16.5 1.0
N A:ASP747 4.0 21.4 1.0
C A:ARG746 4.1 19.1 1.0
N A:LEU745 4.1 17.4 1.0
CA A:ASP747 4.1 21.2 1.0
CA A:LEU745 4.2 17.7 1.0
O A:ARG746 4.3 19.5 1.0
CB A:ASP739 4.3 16.4 1.0
N A:ASP743 4.3 18.5 1.0
OD2 A:ASP747 4.3 23.4 1.0
CB A:ASP747 4.4 20.5 1.0
OD2 A:ASP739 4.4 16.9 1.0
N A:ASN741 4.5 19.4 1.0
O A:PHE738 4.5 19.5 1.0
C A:ASP739 4.5 18.7 1.0
CB A:LEU745 4.5 18.5 1.0
N A:ARG746 4.5 18.1 1.0
CB A:ASP743 4.6 22.2 1.0
O A:HOH1280 4.6 43.9 1.0
CA A:ARG746 4.6 18.3 1.0
CB A:ASN741 4.7 21.6 1.0
N A:TYR742 4.7 20.3 1.0
N A:TYR740 4.7 19.1 1.0
C A:ASN741 4.8 20.2 1.0
OE2 A:GLU751 4.8 41.7 1.0
CA A:ASP743 4.8 20.6 1.0
N A:GLY744 4.9 22.5 1.0
CA A:ASN741 4.9 21.2 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: Wed Jul 9 09:45:39 2025

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