Atomistry » Zinc » PDB 5rmk-5sep » 5s9m
Atomistry »
  Zinc »
    PDB 5rmk-5sep »
      5s9m »

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

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy