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

Zinc Binding Sites:

The binding sites of Zinc 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 Zinc atom.
In total only one binding site of Zinc was 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:

Zinc binding site 1 out of 1 in 5s9n

Go back to Zinc Binding Sites List in 5s9n
Zinc binding site 1 out of 1 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 Zinc with other atoms in the Zn 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:Zn902

b:24.1
occ:1.00
 N19 A:YVS901 1.8 36.6 1.0
OD1 A:ASP311 1.9 21.4 1.0
NE2 A:HIS474 2.0 21.4 1.0
NE2 A:HIS315 2.1 21.8 1.0
N20 A:YVS901 2.3 40.4 1.0
OD2 A:ASP311 2.5 23.8 1.0
CG A:ASP311 2.6 20.3 1.0
CD2 A:HIS315 3.0 22.3 1.0
CE1 A:HIS474 3.0 21.5 1.0
CD2 A:HIS474 3.1 19.4 1.0
C18 A:YVS901 3.1 42.2 1.0
CE1 A:HIS315 3.2 24.4 1.0
N21 A:YVS901 3.6 49.0 1.0
C15 A:YVS901 4.0 36.1 1.0
C17 A:YVS901 4.1 44.6 1.0
CB A:ASP311 4.1 19.9 1.0
OG1 A:THR209 4.1 27.2 1.0
CE1 A:HIS359 4.1 19.5 1.0
ND1 A:HIS474 4.1 18.2 1.0
CG A:HIS474 4.2 16.6 1.0
CG A:HIS315 4.2 21.4 1.0
ND1 A:HIS315 4.2 22.2 1.0
CE A:MET361 4.4 22.3 1.0
OD2 A:ASP171 4.4 30.9 1.0
NE2 A:HIS359 4.4 19.5 1.0
O A:HOH1002 4.6 29.4 1.0
OD1 A:ASP171 4.8 25.3 1.0
O A:ASP311 4.9 20.2 1.0
CG A:ASP171 4.9 27.8 1.0
CA A:ASP311 5.0 22.5 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: Fri Apr 7 21:35:46 2023

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