Atomistry » Fluorine » PDB 5rza-5say » 5s9n
Atomistry »
  Fluorine »
    PDB 5rza-5say »
      5s9n »

Fluorine 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
Calcium (Ca) 2 atoms
Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine 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 Fluorine atom.
In total 3 binding sites of Fluorine 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 Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5s9n

Go back to Fluorine Binding Sites List in 5s9n
Fluorine binding site 1 out of 3 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 Fluorine with other atoms in the F 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:F901

b:55.2
occ:1.00
 F34 A:YVS901 0.0 55.2 1.0
C33 A:YVS901 1.4 51.0 1.0
F35 A:YVS901 2.2 47.0 1.0
F36 A:YVS901 2.2 53.8 1.0
O32 A:YVS901 2.4 43.0 1.0
C29 A:YVS901 2.9 50.1 1.0
C30 A:YVS901 3.1 45.1 1.0
CB A:ALA217 3.2 20.1 1.0
CD2 A:PHE273 3.4 30.9 1.0
CA A:ALA217 3.5 18.4 1.0
CE2 A:PHE273 3.5 30.9 1.0
CZ3 A:TRP260 3.8 27.8 1.0
N A:ALA217 3.8 17.8 1.0
C28 A:YVS901 4.0 47.0 1.0
C31 A:YVS901 4.2 51.9 1.0
CE3 A:TRP260 4.4 27.4 1.0
O A:LEU213 4.5 17.1 1.0
C A:LEU216 4.5 21.1 1.0
CG A:PHE273 4.8 34.0 1.0
C A:ALA217 4.8 18.0 1.0
O A:LEU216 4.8 21.2 1.0
CH2 A:TRP260 4.9 29.9 1.0
CZ A:PHE273 4.9 32.0 1.0
CB A:LEU216 4.9 19.3 1.0
C27 A:YVS901 5.0 49.5 1.0

Fluorine binding site 2 out of 3 in 5s9n

Go back to Fluorine Binding Sites List in 5s9n
Fluorine binding site 2 out of 3 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 Fluorine with other atoms in the F 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:F901

b:47.0
occ:1.00
 F35 A:YVS901 0.0 47.0 1.0
C33 A:YVS901 1.3 51.0 1.0
F34 A:YVS901 2.2 55.2 1.0
F36 A:YVS901 2.2 53.8 1.0
O32 A:YVS901 2.2 43.0 1.0
CB A:LEU216 3.4 19.3 1.0
C29 A:YVS901 3.5 50.1 1.0
C A:LEU216 3.5 21.1 1.0
N A:ALA217 3.6 17.8 1.0
O A:LEU216 3.8 21.2 1.0
CA A:ALA217 3.8 18.4 1.0
CE A:MET512 3.9 22.1 1.0
CA A:LEU216 4.1 20.3 1.0
C30 A:YVS901 4.2 45.1 1.0
CB A:ALA217 4.3 20.1 1.0
SD A:MET512 4.4 25.2 1.0
C28 A:YVS901 4.4 47.0 1.0
CG2 A:ILE167 4.5 21.6 1.0
O A:LEU213 4.5 17.1 1.0
CD1 A:ILE167 4.7 31.0 1.0
CG A:LEU216 4.7 23.3 1.0
CD1 A:LEU216 4.9 25.4 1.0
CE2 A:PHE273 4.9 30.9 1.0

Fluorine binding site 3 out of 3 in 5s9n

Go back to Fluorine Binding Sites List in 5s9n
Fluorine binding site 3 out of 3 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 Fluorine with other atoms in the F binding site number 3 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:F901

b:53.8
occ:1.00
 F36 A:YVS901 0.0 53.8 1.0
C33 A:YVS901 1.3 51.0 1.0
F35 A:YVS901 2.2 47.0 1.0
O32 A:YVS901 2.2 43.0 1.0
F34 A:YVS901 2.2 55.2 1.0
C29 A:YVS901 2.8 50.1 1.0
C28 A:YVS901 3.2 47.0 1.0
CE2 A:PHE273 3.4 30.9 1.0
CD1 A:ILE167 3.5 31.0 1.0
CG2 A:ILE167 3.5 21.6 1.0
CD2 A:PHE273 3.6 30.9 1.0
C30 A:YVS901 3.8 45.1 1.0
CB A:ILE167 4.0 20.3 1.0
CG1 A:ILE167 4.3 24.6 1.0
CB A:ALA304 4.3 23.6 1.0
C27 A:YVS901 4.4 49.5 1.0
CZ A:PHE273 4.7 32.0 1.0
C31 A:YVS901 4.8 51.9 1.0
CG A:PHE273 4.9 34.0 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: Thu Aug 1 14:09:06 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy