Atomistry » Sodium » PDB 7g6y-7gnp » 7g7z
Atomistry »
  Sodium »
    PDB 7g6y-7gnp »
      7g7z »

Sodium 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:

Calcium (Ca) 2 atoms
Zinc (Zn) 1 atom
Fluorine (F) 7 atoms

Sodium Binding Sites:

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

Sodium binding site 1 out of 2 in 7g7z

Go back to Sodium Binding Sites List in 7g7z
Sodium 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 Sodium with other atoms in the Na 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:Na904

b:33.0
occ:1.00
 O A:HOH1380 2.2 39.5 1.0
O A:SER804 2.3 32.4 1.0
OG A:SER807 2.3 34.2 1.0
O A:HOH1322 2.4 40.3 1.0
O A:HOH1084 2.4 35.8 1.0
O A:ASN801 2.5 28.7 1.0
C A:SER804 3.3 33.1 1.0
C A:ASN801 3.4 26.0 1.0
CB A:SER807 3.4 34.2 1.0
CA A:ASP802 3.8 31.4 1.0
N A:ASP802 4.0 27.9 1.0
N A:CYS805 4.1 32.9 1.0
CA A:CYS805 4.1 35.6 1.0
N A:SER807 4.1 34.3 1.0
C A:ASP802 4.2 30.8 1.0
O A:ASP802 4.2 30.8 1.0
CA A:SER807 4.3 34.6 1.0
C A:CYS805 4.3 36.5 1.0
CA A:SER804 4.3 29.9 1.0
N A:SER804 4.3 28.4 1.0
CB A:ASN801 4.4 27.8 1.0
CA A:ASN801 4.5 28.7 1.0
O A:CYS805 4.5 40.9 1.0
OD1 A:ASP802 4.6 35.9 1.0
O A:HOH1170 4.7 35.5 1.0
CB A:SER804 4.8 30.5 1.0
O A:HOH1263 4.9 39.3 1.0
N A:ASN806 4.9 35.4 1.0
N A:GLU803 5.0 27.6 1.0

Sodium binding site 2 out of 2 in 7g7z

Go back to Sodium Binding Sites List in 7g7z
Sodium 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 Sodium with other atoms in the Na 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:Na906

b:25.6
occ:1.00
 O A:ASP672 2.2 34.8 1.0
O A:HOH1364 2.2 43.8 1.0
O A:MET675 2.3 34.8 1.0
O A:HOH1307 2.3 42.0 1.0
O A:TYR669 2.3 33.9 1.0
C A:MET675 3.4 35.8 1.0
C A:ASP672 3.4 38.0 1.0
C A:TYR669 3.5 36.9 1.0
N A:MET675 4.1 39.3 1.0
N A:SER676 4.2 31.2 1.0
N A:LYS673 4.3 39.9 1.0
CA A:TYR669 4.3 34.1 1.0
CA A:SER676 4.3 30.1 1.0
CA A:LYS673 4.3 43.6 1.0
CA A:MET675 4.3 36.2 1.0
O A:LYS670 4.3 40.4 1.0
CA A:ASP672 4.4 38.5 1.0
C A:LYS673 4.4 43.7 1.0
N A:LYS670 4.5 40.3 1.0
N A:ASP672 4.5 41.1 1.0
CB A:ASP672 4.5 38.6 1.0
O A:LYS673 4.6 41.6 1.0
C A:LYS670 4.6 38.5 1.0
CA A:LYS670 4.6 41.1 1.0
CB A:TYR669 4.7 31.8 1.0
N A:GLN674 4.8 42.1 1.0
CB A:SER676 4.9 31.7 1.0
C A:GLN674 5.0 41.7 1.0
CB A:MET675 5.0 35.1 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: Sat Feb 8 23:37:45 2025

Last articles

Zn in 9IRQ
Zn in 9IYX
Zn in 9J8P
Zn in 9IUU
Zn in 9GBF
Zn in 9G2V
Zn in 9G2L
Zn in 9G2X
Zn in 9G2Z
Zn in 9G2K
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy