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Zinc in PDB 5s9m: Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%

Enzymatic activity of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%

All present enzymatic activity of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%:
3.1.4.39;

Protein crystallography data

The structure of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%, PDB code: 5s9m 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) 48.37 / 1.80
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.017, 91.009, 119.028, 90, 90, 90
R / Rfree (%) 17.1 / 21.1

Other elements in 5s9m:

The structure of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Calcium (Ca) 3 atoms
Sodium (Na) 1 atom

Zinc Binding Sites:

The binding sites of Zinc atom in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% (pdb code 5s9m). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%, PDB code: 5s9m:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 5s9m

Go back to Zinc Binding Sites List in 5s9m
Zinc binding site 1 out of 2 in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn907

b:21.6
occ:1.00
 N33 A:YV1901 1.9 23.9 1.0
OD2 A:ASP311 2.0 20.5 1.0
NE2 A:HIS315 2.0 19.8 1.0
NE2 A:HIS474 2.1 21.4 1.0
CG A:ASP311 2.7 20.9 1.0
OD1 A:ASP311 2.8 23.1 1.0
N34 A:YV1901 2.8 31.9 1.0
C32 A:YV1901 3.0 27.6 1.0
CD2 A:HIS315 3.0 21.0 1.0
CE1 A:HIS315 3.0 20.8 1.0
CD2 A:HIS474 3.1 19.2 1.0
CE1 A:HIS474 3.1 18.7 1.0
C29 A:YV1901 3.6 27.2 1.0
N35 A:YV1901 4.0 31.6 1.0
C31 A:YV1901 4.1 28.1 1.0
O A:HOH1001 4.1 24.0 1.0
CE1 A:HIS359 4.1 19.1 1.0
ND1 A:HIS315 4.1 20.6 1.0
CG A:HIS315 4.2 20.7 1.0
CB A:ASP311 4.2 18.1 1.0
ND1 A:HIS474 4.2 18.5 1.0
CG A:HIS474 4.2 18.1 1.0
CE A:MET361 4.4 18.5 1.0
OG1 A:THR209 4.4 22.0 1.0
O A:HOH1213 4.4 49.3 1.0
CA A:CA909 4.4 26.2 0.4
NE2 A:HIS359 4.4 19.9 1.0
ZN A:ZN908 4.5 24.6 0.6
OD1 A:ASP171 4.6 21.4 1.0
O A:ASP311 4.9 19.4 1.0
CA A:ASP311 5.0 19.3 1.0

Zinc binding site 2 out of 2 in 5s9m

Go back to Zinc Binding Sites List in 5s9m
Zinc binding site 2 out of 2 in the Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1%


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Autotaxin, (3,5-Dichlorophenyl)Methyl (3AS,8AR)-2-(1H-Benzotriazole-5- Carbonyl)-1,3,3A,4,5,7,8,8A-Octahydropyrrolo[3,4-D]Azepine-6- Carboxylate, 1.80A, P212121, Rfree=21.1% within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn908

b:24.6
occ:0.60
 CA A:CA909 0.2 26.2 0.4
OD1 A:ASP171 2.0 21.4 1.0
OG1 A:THR209 2.0 22.0 1.0
NE2 A:HIS359 2.1 19.9 1.0
OD2 A:ASP358 2.1 24.7 1.0
CG A:ASP171 2.8 22.2 1.0
CB A:THR209 2.9 21.1 1.0
CD2 A:HIS359 3.0 17.8 1.0
CG A:ASP358 3.0 22.7 1.0
OD2 A:ASP171 3.0 27.4 1.0
CE1 A:HIS359 3.0 19.1 1.0
CG2 A:THR209 3.2 22.3 1.0
OD1 A:ASP358 3.3 20.1 1.0
CA A:THR209 3.4 18.3 1.0
N A:THR209 3.9 16.3 1.0
O A:HOH1001 4.0 24.0 1.0
OD2 A:ASP311 4.1 20.5 1.0
ND1 A:HIS359 4.1 18.9 1.0
CG A:HIS359 4.1 18.7 1.0
CB A:ASP171 4.1 19.6 1.0
C29 A:YV1901 4.1 27.2 1.0
N A:GLY172 4.2 18.1 1.0
CE1 A:HIS474 4.2 18.7 1.0
CB A:ASP358 4.3 19.0 1.0
CA A:ASP171 4.4 19.5 1.0
CG A:ASP311 4.5 20.9 1.0
ZN A:ZN907 4.5 21.6 1.0
NE2 A:HIS474 4.6 21.4 1.0
C32 A:YV1901 4.6 27.6 1.0
N33 A:YV1901 4.7 23.9 1.0
C A:ASP171 4.7 21.1 1.0
C A:THR209 4.7 19.9 1.0
C A:LYS208 4.7 18.0 1.0
C28 A:YV1901 4.9 28.7 1.0
CB A:ASP311 4.9 18.1 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: Mon Oct 28 04:29:04 2024

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