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Chlorine 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:

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

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total 4 binding sites of Chlorine 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 Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in 5s9n

Go back to Chlorine Binding Sites List in 5s9n
Chlorine binding site 1 out of 4 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 Chlorine with other atoms in the Cl 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:Cl905

b:52.6
occ:1.00
 NH1 A:ARG746 2.9 30.3 1.0
O A:HOH1359 3.0 46.6 1.0
O A:HOH1095 3.1 37.4 1.0
NH2 A:ARG746 3.4 31.7 1.0
CZ A:ARG746 3.6 38.6 1.0
CA A:THR748 3.9 25.4 1.0
N A:GLU749 3.9 25.2 1.0
CE1 A:PHE625 4.1 29.9 1.0
CB A:THR748 4.2 28.4 1.0
CE2 A:TYR605 4.3 20.8 1.0
C A:THR748 4.4 27.4 1.0
CG2 A:THR748 4.5 30.2 1.0
CD2 A:TYR605 4.5 21.6 1.0
CZ A:PHE625 4.5 23.6 1.0
O A:ASP747 4.7 22.6 1.0
CB A:GLU749 4.8 39.8 1.0
O A:ARG606 4.9 23.8 1.0
CA A:GLU749 4.9 34.9 1.0
NE A:ARG746 4.9 40.5 1.0

Chlorine binding site 2 out of 4 in 5s9n

Go back to Chlorine Binding Sites List in 5s9n
Chlorine binding site 2 out of 4 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 Chlorine with other atoms in the Cl 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:Cl906

b:41.6
occ:1.00
 N A:ASN230 3.2 28.6 1.0
NH1 A:ARG391 3.3 26.5 1.0
CA A:GLY229 3.5 25.9 1.0
NZ A:LYS208 3.5 40.1 1.0
N A:SER231 3.8 31.8 1.0
C A:GLY229 3.8 27.4 1.0
O A:SER231 4.1 26.7 1.0
CG1 A:VAL385 4.2 31.4 1.0
CA A:ASN230 4.2 34.0 1.0
CD1 A:LEU389 4.4 34.6 1.0
CZ A:ARG391 4.4 28.0 1.0
CD2 A:LEU389 4.5 36.3 1.0
CB A:ASN230 4.5 35.8 1.0
C A:ASN230 4.6 35.7 1.0
CG A:LYS208 4.6 25.5 1.0
CG A:LEU389 4.7 29.1 1.0
O A:HOH1241 4.7 39.5 1.0
NH2 A:ARG391 4.7 28.9 1.0
CA A:SER231 4.7 34.4 1.0
CB A:SER231 4.8 37.1 1.0
N A:GLY229 4.9 22.8 1.0
C A:SER231 4.9 27.1 1.0
CE A:LYS208 4.9 36.4 1.0

Chlorine binding site 3 out of 4 in 5s9n

Go back to Chlorine Binding Sites List in 5s9n
Chlorine binding site 3 out of 4 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 Chlorine with other atoms in the Cl 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:Cl907

b:58.6
occ:1.00
 O A:HOH1136 2.8 44.8 1.0
NH2 A:ARG174 3.0 28.6 1.0
O A:HOH1353 3.1 34.7 1.0
OG A:SER176 3.7 25.2 1.0
NE A:ARG174 3.8 24.8 1.0
CZ A:ARG174 3.9 27.9 1.0
CG2 A:ILE862 4.0 80.0 1.0
CB A:SER176 4.0 25.0 1.0
N A:GLY863 4.1 80.0 1.0
CB A:ASN481 4.2 28.7 1.0
O A:ASN481 4.3 19.5 1.0
C A:ASN481 4.5 19.1 1.0
CA A:ILE862 4.6 80.0 1.0
CD1 A:ILE862 4.7 69.8 1.0
CB A:ILE862 4.7 80.0 1.0
O A:GLY863 4.7 80.0 1.0
CG A:ASN481 4.8 43.8 1.0
N A:SER482 4.8 16.6 1.0
C A:ILE862 4.8 80.0 1.0
ND2 A:ASN481 4.8 44.6 1.0
O A:HOH1220 4.9 44.0 1.0
CA A:SER482 4.9 17.7 1.0
CA A:GLY863 4.9 80.0 1.0
CG1 A:ILE862 5.0 80.0 1.0
CA A:ASN481 5.0 21.3 1.0

Chlorine binding site 4 out of 4 in 5s9n

Go back to Chlorine Binding Sites List in 5s9n
Chlorine binding site 4 out of 4 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 Chlorine with other atoms in the Cl binding site number 4 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:Cl908

b:51.1
occ:1.00
 ND2 A:ASN801 3.0 25.3 1.0
NH2 A:ARG710 3.1 31.6 1.0
O A:HOH1173 3.2 38.5 1.0
O A:HOH1019 3.2 41.2 1.0
CD A:ARG710 3.8 28.2 1.0
CG A:ASN801 3.9 26.1 1.0
CB A:ALA707 4.0 25.9 1.0
CB A:ASN801 4.0 22.4 1.0
CA A:ALA707 4.2 21.2 1.0
CZ A:ARG710 4.2 28.6 1.0
N A:ASN801 4.4 22.1 1.0
NE A:ARG710 4.5 31.5 1.0
O A:ALA707 4.7 22.9 1.0
CA A:ASN801 4.8 22.9 1.0
OG A:SER807 4.9 27.8 1.0
C A:ALA707 4.9 20.3 1.0
CG A:ARG710 5.0 29.4 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 Jul 12 08:19:09 2025

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