Atomistry » Calcium » PDB 7g78-7jlg » 7g7z
Atomistry »
  Calcium »
    PDB 7g78-7jlg »
      7g7z »

Calcium in PDB 7g7z: Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid, PDB code: 7g7z was solved by M.Stihle, J.Benz, D.Hunziker, P.Mattei, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.97 / 1.79
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.096, 92.112, 120.482, 90, 90, 90
R / Rfree (%) 20.2 / 24.2

Other elements in 7g7z:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid also contains other interesting chemical elements:

Sodium (Na) 2 atoms
Zinc (Zn) 1 atom
Fluorine (F) 7 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid (pdb code 7g7z). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid, PDB code: 7g7z:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in 7g7z

Go back to Calcium Binding Sites List in 7g7z
Calcium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca901

b:42.5
occ:1.00
 OD1 A:ASP171 1.7 35.5 1.0
OG1 A:THR209 1.9 32.6 1.0
NE2 A:HIS359 2.1 27.2 1.0
OD2 A:ASP358 2.3 29.3 1.0
CG A:ASP171 2.6 31.9 1.0
CE1 A:HIS359 2.9 27.3 1.0
OD2 A:ASP171 2.9 46.8 1.0
CB A:THR209 2.9 27.9 1.0
CD2 A:HIS359 3.1 26.4 1.0
CG A:ASP358 3.1 26.2 1.0
CG2 A:THR209 3.3 28.9 1.0
OD1 A:ASP358 3.3 24.9 1.0
CA A:THR209 3.3 26.8 1.0
O A:HOH1082 3.6 37.1 1.0
N A:THR209 3.8 26.6 1.0
CB A:ASP171 3.9 29.8 1.0
ND1 A:HIS359 4.0 26.2 1.0
CG A:HIS359 4.1 26.1 1.0
N A:GLY172 4.2 24.6 1.0
OD1 A:ASP311 4.2 29.3 1.0
CA A:ASP171 4.2 27.9 1.0
O A:HOH1007 4.3 30.8 1.0
CB A:ASP358 4.4 24.9 1.0
CG A:ASP311 4.5 28.9 1.0
O A:HOH1342 4.5 26.2 1.0
CE1 A:HIS474 4.5 27.1 1.0
ZN A:ZN903 4.5 28.3 1.0
C A:ASP171 4.6 26.6 1.0
NE2 A:HIS474 4.6 29.0 1.0
C A:THR209 4.7 25.8 1.0
C A:LYS208 4.7 25.2 1.0
CB A:ASP311 4.8 28.3 1.0
OD2 A:ASP311 4.9 33.8 1.0
OH A:TYR306 5.0 33.1 1.0

Calcium binding site 2 out of 2 in 7g7z

Go back to Calcium Binding Sites List in 7g7z
Calcium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Rat Autotaxin in Complex with 3-Fluoro-4-[1-[3- [2-[(5-Methyltetrazol-2-Yl)Methyl]-4-(Trifluoromethyl) Phenyl]Propanoyl]Piperidin-4-Yl]Sulfanylbenzoic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca905

b:24.6
occ:1.00
 O A:LEU745 2.3 22.9 1.0
OD1 A:ASP739 2.3 24.7 1.0
OD1 A:ASP747 2.3 23.8 1.0
OD1 A:ASP743 2.3 26.1 1.0
OD1 A:ASN741 2.4 25.8 1.0
O A:HOH1235 2.4 26.6 1.0
CG A:ASP743 3.3 26.5 1.0
CG A:ASN741 3.4 28.5 1.0
CG A:ASP739 3.4 23.6 1.0
C A:LEU745 3.5 24.1 1.0
CG A:ASP747 3.5 25.1 1.0
OD2 A:ASP743 3.6 27.6 1.0
ND2 A:ASN741 3.8 29.0 1.0
CA A:ASP739 3.9 22.9 1.0
N A:ASP747 3.9 23.8 1.0
C A:ARG746 4.1 22.6 1.0
N A:LEU745 4.1 22.8 1.0
CA A:ASP747 4.1 24.4 1.0
CB A:ASP739 4.2 23.1 1.0
O A:ARG746 4.2 23.1 1.0
CA A:LEU745 4.2 23.0 1.0
N A:ASP743 4.3 23.5 1.0
OD2 A:ASP739 4.3 23.9 1.0
O A:PHE738 4.4 23.2 1.0
CB A:ASP747 4.4 24.5 1.0
OD2 A:ASP747 4.4 26.5 1.0
CB A:LEU745 4.5 26.1 1.0
C A:ASP739 4.5 25.8 1.0
N A:ARG746 4.5 20.6 1.0
CB A:ASP743 4.5 26.4 1.0
N A:ASN741 4.5 25.3 1.0
O A:HOH1236 4.5 38.0 1.0
OE2 A:GLU751 4.6 38.3 1.0
CB A:ASN741 4.7 27.0 1.0
N A:TYR740 4.7 26.3 1.0
CA A:ARG746 4.7 23.6 1.0
N A:TYR742 4.8 26.7 1.0
CA A:ASP743 4.8 24.4 1.0
N A:GLY744 4.9 23.9 1.0
C A:ASN741 4.9 26.4 1.0
CA A:ASN741 4.9 28.1 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: Wed Jul 9 22:40:30 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy