Atomistry » Sodium » PDB 7g49-7g5t » 7g49
Atomistry »
  Sodium »
    PDB 7g49-7g5t »
      7g49 »

Sodium in PDB 7g49: Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One, PDB code: 7g49 was solved by M.Stihle, J.Benz, D.Hunziker, E.Goetschi, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.03 / 1.90
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.899, 92.064, 119.722, 90, 90, 90
R / Rfree (%) 16 / 20.8

Other elements in 7g49:

The structure of Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One also contains other interesting chemical elements:

Calcium (Ca) 1 atom
Chlorine (Cl) 1 atom
Zinc (Zn) 1 atom
Fluorine (F) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One (pdb code 7g49). 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 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One, PDB code: 7g49:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g49

Go back to Sodium Binding Sites List in 7g49
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One


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 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na904

b:30.2
occ:1.00
 O A:TYR669 2.2 29.3 1.0
O A:MET675 2.2 25.7 1.0
O A:ASP672 2.4 30.8 1.0
O A:HOH1460 2.5 37.2 1.0
O A:HOH1510 2.5 47.4 1.0
O A:HOH1545 2.9 35.5 1.0
C A:TYR669 3.4 31.5 1.0
C A:MET675 3.4 29.1 1.0
C A:ASP672 3.5 34.0 1.0
H A:MET675 3.6 34.2 1.0
HA A:SER676 3.6 30.2 1.0
HA A:TYR669 3.8 31.7 1.0
HB3 A:TYR669 3.9 32.5 1.0
HA A:LYS673 3.9 42.0 1.0
HB3 A:ASP672 4.0 34.7 1.0
CA A:TYR669 4.1 26.4 1.0
N A:MET675 4.1 28.5 1.0
HA A:LYS670 4.2 33.6 1.0
H A:ASP672 4.3 40.6 1.0
N A:SER676 4.3 20.6 1.0
CA A:MET675 4.3 21.9 1.0
O A:LYS670 4.3 34.3 1.0
HB3 A:MET675 4.4 26.4 1.0
N A:LYS670 4.4 27.2 1.0
CA A:SER676 4.4 25.2 1.0
N A:LYS673 4.4 29.4 1.0
CA A:LYS673 4.4 35.0 1.0
CA A:ASP672 4.4 26.2 1.0
HD1 A:TYR669 4.5 24.0 1.0
CB A:TYR669 4.5 27.1 1.0
O A:HOH1589 4.5 38.7 1.0
C A:LYS673 4.5 33.1 1.0
N A:ASP672 4.5 33.8 1.0
C A:LYS670 4.5 25.2 1.0
CA A:LYS670 4.6 28.0 1.0
HB2 A:SER676 4.6 28.2 1.0
O A:LYS673 4.7 34.4 1.0
CB A:ASP672 4.7 28.9 1.0
CB A:MET675 4.9 22.0 1.0
N A:GLN674 4.9 25.3 1.0

Sodium binding site 2 out of 2 in 7g49

Go back to Sodium Binding Sites List in 7g49
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One


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 8-(2-Fluorophenyl)- 4-[3-(5-Methyl-1,3,4-Oxadiazol-2-Yl)Phenyl]-1,3-Dihydro-1,5- Benzodiazepin-2-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na906

b:29.2
occ:1.00
 HG A:SER807 2.2 26.2 1.0
O A:HOH1515 2.3 28.1 1.0
OG A:SER807 2.4 21.9 1.0
O A:SER804 2.4 18.5 1.0
O A:HOH1145 2.5 23.8 1.0
O A:ASN801 2.5 21.4 1.0
O A:HOH1210 2.5 28.3 1.0
HA A:ASP802 3.0 25.0 1.0
H A:SER807 3.3 27.2 1.0
C A:ASN801 3.3 21.4 1.0
C A:SER804 3.4 28.1 1.0
HB3 A:SER807 3.5 25.2 1.0
CB A:SER807 3.5 21.0 1.0
HA A:CYS805 3.6 28.6 1.0
CA A:ASP802 3.7 20.8 1.0
H A:SER804 3.8 25.1 1.0
N A:ASP802 3.9 20.0 1.0
HB3 A:ASN801 4.0 27.2 1.0
N A:SER807 4.1 22.6 1.0
HB2 A:SER804 4.1 31.2 1.0
C A:ASP802 4.1 21.9 1.0
O A:ASP802 4.1 23.4 1.0
HB2 A:ASN801 4.1 27.2 1.0
CA A:CYS805 4.2 23.8 1.0
HB2 A:SER807 4.2 25.2 1.0
N A:CYS805 4.2 25.4 1.0
N A:SER804 4.2 20.9 1.0
C A:CYS805 4.3 25.5 1.0
CA A:SER804 4.3 22.5 1.0
O A:CYS805 4.3 25.6 1.0
CA A:SER807 4.3 24.3 1.0
CB A:ASN801 4.4 22.7 1.0
CA A:ASN801 4.4 22.9 1.0
O A:HOH1317 4.4 32.2 1.0
OD1 A:ASP802 4.6 28.8 1.0
H A:ASP802 4.7 23.9 1.0
CB A:SER804 4.7 26.0 1.0
O A:HOH1065 4.7 28.6 1.0
N A:ASN806 4.8 24.1 1.0
H A:ASN801 4.8 22.9 1.0
H A:SER808 4.9 34.6 1.0
N A:GLU803 4.9 18.4 1.0
O A:HOH1392 5.0 31.1 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 23:18:35 2025

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy