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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

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