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Calcium 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:

Zinc (Zn) 2 atoms
Chlorine (Cl) 3 atoms
Sodium (Na) 1 atom

Calcium Binding Sites:

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

Calcium binding site 1 out of 3 in 5s9m

Go back to Calcium Binding Sites List in 5s9m
Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca909

b:26.2
occ:0.40
 ZN A:ZN908 0.2 24.6 0.6
OD1 A:ASP171 1.8 21.4 1.0
OG1 A:THR209 2.1 22.0 1.0
NE2 A:HIS359 2.1 19.9 1.0
OD2 A:ASP358 2.2 24.7 1.0
CG A:ASP171 2.7 22.2 1.0
OD2 A:ASP171 2.9 27.4 1.0
CE1 A:HIS359 3.0 19.1 1.0
CB A:THR209 3.0 21.1 1.0
CG A:ASP358 3.1 22.7 1.0
CD2 A:HIS359 3.1 17.8 1.0
CG2 A:THR209 3.2 22.3 1.0
OD1 A:ASP358 3.3 20.1 1.0
CA A:THR209 3.5 18.3 1.0
OD2 A:ASP311 3.9 20.5 1.0
CB A:ASP171 4.0 19.6 1.0
O A:HOH1001 4.0 24.0 1.0
C29 A:YV1901 4.0 27.2 1.0
N A:THR209 4.1 16.3 1.0
ND1 A:HIS359 4.1 18.9 1.0
N A:GLY172 4.1 18.1 1.0
CG A:HIS359 4.2 18.7 1.0
CE1 A:HIS474 4.3 18.7 1.0
CA A:ASP171 4.3 19.5 1.0
CG A:ASP311 4.4 20.9 1.0
ZN A:ZN907 4.4 21.6 1.0
CB A:ASP358 4.5 19.0 1.0
C32 A:YV1901 4.5 27.6 1.0
NE2 A:HIS474 4.5 21.4 1.0
C A:ASP171 4.6 21.1 1.0
N33 A:YV1901 4.6 23.9 1.0
CB A:ASP311 4.8 18.1 1.0
C A:THR209 4.8 19.9 1.0
C28 A:YV1901 4.8 28.7 1.0
C A:LYS208 4.9 18.0 1.0
OD1 A:ASP311 4.9 23.1 1.0
CA A:GLY172 5.0 20.3 1.0

Calcium binding site 2 out of 3 in 5s9m

Go back to Calcium Binding Sites List in 5s9m
Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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:Ca910

b:28.0
occ:1.00
 O A:TYR669 2.2 25.5 1.0
O A:ASP672 2.3 23.1 1.0
O A:HOH1399 2.3 37.7 1.0
O A:MET675 2.3 24.5 1.0
O A:HOH1247 2.3 30.3 1.0
O A:HOH1420 2.5 35.0 1.0
C A:TYR669 3.4 28.7 1.0
C A:ASP672 3.5 26.6 1.0
C A:MET675 3.5 24.4 1.0
N A:MET675 4.1 23.6 1.0
CA A:TYR669 4.2 23.9 1.0
O A:LYS670 4.3 33.1 1.0
O A:HOH1143 4.3 42.3 1.0
CA A:ASP672 4.4 26.2 1.0
CA A:LYS673 4.4 31.2 1.0
CA A:MET675 4.4 22.4 1.0
N A:SER676 4.4 20.3 1.0
N A:LYS670 4.4 28.1 1.0
N A:LYS673 4.4 28.3 1.0
CA A:SER676 4.4 21.4 1.0
N A:ASP672 4.4 28.2 1.0
C A:LYS673 4.5 27.7 1.0
CA A:LYS670 4.6 35.1 1.0
CB A:ASP672 4.6 25.4 1.0
C A:LYS670 4.6 34.6 1.0
CB A:TYR669 4.7 22.2 1.0
N A:GLN674 4.8 27.8 1.0
O A:LYS673 4.9 28.5 1.0
C A:GLN674 4.9 31.6 1.0
CB A:MET675 5.0 22.3 1.0

Calcium binding site 3 out of 3 in 5s9m

Go back to Calcium Binding Sites List in 5s9m
Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca911

b:19.9
occ:1.00
 OD1 A:ASP739 2.3 18.8 1.0
OD1 A:ASN741 2.3 20.2 1.0
OD1 A:ASP747 2.3 19.1 1.0
O A:LEU745 2.3 19.2 1.0
OD1 A:ASP743 2.4 20.6 1.0
O A:HOH1405 2.4 22.9 1.0
CG A:ASP743 3.4 20.1 1.0
CG A:ASN741 3.4 24.3 1.0
CG A:ASP739 3.4 19.4 1.0
C A:LEU745 3.5 20.6 1.0
CG A:ASP747 3.5 18.2 1.0
OD2 A:ASP743 3.8 20.7 1.0
N A:ASP747 3.9 18.4 1.0
ND2 A:ASN741 3.9 24.4 1.0
CA A:ASP739 3.9 17.4 1.0
C A:ARG746 4.1 18.5 1.0
N A:LEU745 4.1 17.7 1.0
CA A:ASP747 4.1 17.9 1.0
CB A:ASP739 4.2 19.1 1.0
CA A:LEU745 4.2 18.9 1.0
O A:ARG746 4.2 19.3 1.0
N A:ASP743 4.3 17.8 1.0
OD2 A:ASP747 4.4 23.6 1.0
OD2 A:ASP739 4.4 19.1 1.0
O A:PHE738 4.4 18.8 1.0
N A:ASN741 4.4 18.7 1.0
CB A:ASP747 4.4 17.7 1.0
C A:ASP739 4.5 20.2 1.0
OE2 A:GLU751 4.5 42.9 1.0
N A:ARG746 4.5 18.0 1.0
CB A:LEU745 4.5 20.8 1.0
CB A:ASP743 4.6 20.8 1.0
CB A:ASN741 4.7 18.8 1.0
N A:TYR740 4.7 19.5 1.0
CA A:ARG746 4.7 21.2 1.0
N A:TYR742 4.7 19.3 1.0
O A:HOH1378 4.7 44.2 1.0
C A:ASN741 4.8 19.9 1.0
CA A:ASN741 4.8 19.4 1.0
CA A:ASP743 4.9 19.4 1.0
N A:GLY744 4.9 20.4 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: Wed Jul 9 09:45:39 2025

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