Atomistry » Sodium » PDB 7g5u-7g6x » 7g6i
Atomistry »
  Sodium »
    PDB 7g5u-7g6x »
      7g6i »

Sodium in PDB 7g6i: Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm, PDB code: 7g6i was solved by M.Stihle, J.Benz, D.Hunziker, H.Kuhne, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.83 / 1.83
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 84.02, 91.688, 120.003, 90, 90, 90
R / Rfree (%) 18.9 / 23.2

Other elements in 7g6i:

The structure of Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm also contains other interesting chemical elements:

Zinc (Zn) 1 atom
Chlorine (Cl) 2 atoms
Calcium (Ca) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm (pdb code 7g6i). 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 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm, PDB code: 7g6i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g6i

Go back to Sodium Binding Sites List in 7g6i
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm


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 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:37.7
occ:1.00
 OG A:SER807 2.4 25.6 1.0
O A:HOH1236 2.4 33.6 1.0
O A:HOH1473 2.4 34.5 1.0
O A:SER804 2.4 27.3 1.0
O A:HOH1143 2.5 29.4 1.0
O A:ASN801 2.5 28.3 1.0
C A:ASN801 3.4 27.1 1.0
C A:SER804 3.5 28.4 1.0
CB A:SER807 3.5 27.8 1.0
CA A:ASP802 3.9 28.8 1.0
O A:HOH1543 4.0 52.4 1.0
N A:ASP802 4.0 27.6 1.0
N A:SER807 4.1 31.6 1.0
O A:ASP802 4.2 28.6 1.0
CA A:CYS805 4.2 31.9 1.0
C A:ASP802 4.2 29.4 1.0
N A:CYS805 4.3 28.5 1.0
CA A:SER807 4.3 31.1 1.0
O A:HOH1090 4.3 46.9 1.0
C A:CYS805 4.3 32.7 1.0
N A:SER804 4.4 27.1 1.0
CB A:ASN801 4.4 25.6 1.0
CA A:SER804 4.4 27.2 1.0
O A:CYS805 4.5 32.4 1.0
CA A:ASN801 4.5 27.7 1.0
O A:HOH1125 4.5 44.2 1.0
OD1 A:ASP802 4.7 37.0 1.0
CB A:SER804 4.8 29.2 1.0
N A:ASN806 4.9 31.8 1.0
O A:HOH1327 5.0 40.0 1.0

Sodium binding site 2 out of 2 in 7g6i

Go back to Sodium Binding Sites List in 7g6i
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm


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 4-[(2-Tert-Butyl-4- Chloro-5-Methylphenoxy)Methyl]Pyrimidine, I.E. Smiles C1C(NCNC1) COC1CC(C(CC1C(C)(C)C)Cl)C with IC50=0.478806 Microm within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na907

b:23.9
occ:1.00
 O A:HOH1386 1.8 40.6 1.0
O A:ASP672 2.3 32.2 1.0
O A:MET675 2.3 30.2 1.0
O A:TYR669 2.3 35.2 1.0
O A:HOH1341 2.4 34.0 1.0
O A:HOH1489 3.0 42.9 1.0
C A:MET675 3.4 28.1 1.0
C A:TYR669 3.4 32.2 1.0
C A:ASP672 3.5 33.9 1.0
N A:MET675 4.1 31.7 1.0
CA A:TYR669 4.2 29.3 1.0
N A:SER676 4.2 26.4 1.0
O A:LYS670 4.3 36.5 1.0
CA A:SER676 4.3 26.1 1.0
O A:HOH1509 4.3 50.5 1.0
CA A:LYS673 4.3 37.7 1.0
CA A:MET675 4.3 29.1 1.0
N A:LYS673 4.3 35.1 1.0
C A:LYS673 4.4 34.7 1.0
N A:LYS670 4.4 34.8 1.0
CA A:ASP672 4.5 34.0 1.0
O A:LYS673 4.6 37.7 1.0
CB A:TYR669 4.6 28.1 1.0
CA A:LYS670 4.6 36.6 1.0
C A:LYS670 4.6 34.8 1.0
N A:ASP672 4.6 36.5 1.0
CB A:ASP672 4.7 32.6 1.0
CB A:SER676 4.9 26.8 1.0
N A:GLN674 4.9 35.8 1.0
C A:GLN674 4.9 36.8 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 23:28:33 2025

Last articles

Zn in 8S6Z
Zn in 8S4F
Zn in 8RR4
Zn in 8RR3
Zn in 8RR1
Zn in 8RIP
Zn in 8RL5
Zn in 8RIO
Zn in 8RL9
Zn in 8RLA
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy