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Sodium in PDB 7g47: Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One

Enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One

All present enzymatic activity of Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One:
3.1.4.39;

Protein crystallography data

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One, PDB code: 7g47 was solved by M.Stihle, J.Benz, D.Hunziker, H.Richter, M.G.Rudolph, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.45 / 1.94
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 83.858, 91.338, 118.705, 90, 90, 90
R / Rfree (%) 18.2 / 21.8

Other elements in 7g47:

The structure of Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One also contains other interesting chemical elements:

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

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One (pdb code 7g47). 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-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One, PDB code: 7g47:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7g47

Go back to Sodium Binding Sites List in 7g47
Sodium binding site 1 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-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 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na903

b:30.0
occ:1.00
 OG A:SER807 2.3 26.3 1.0
O A:SER804 2.3 25.5 1.0
O A:HOH1256 2.4 28.2 1.0
O A:HOH1193 2.4 32.1 1.0
O A:HOH1386 2.4 30.1 1.0
O A:ASN801 2.6 25.8 1.0
C A:SER804 3.4 27.1 1.0
C A:ASN801 3.4 24.6 1.0
CB A:SER807 3.4 27.7 1.0
N A:SER807 3.9 27.8 1.0
CA A:ASP802 3.9 26.6 1.0
N A:ASP802 4.0 23.8 1.0
CA A:SER807 4.2 29.2 1.0
N A:CYS805 4.2 28.5 1.0
CA A:CYS805 4.2 31.0 1.0
O A:ASP802 4.2 26.7 1.0
C A:ASP802 4.3 26.2 1.0
O A:HOH1104 4.3 38.5 1.0
C A:CYS805 4.3 31.2 1.0
CA A:SER804 4.3 24.0 1.0
CB A:ASN801 4.3 26.2 1.0
O A:CYS805 4.3 32.0 1.0
N A:SER804 4.4 24.9 1.0
CA A:ASN801 4.4 26.7 1.0
O A:HOH1180 4.6 41.7 1.0
CB A:SER804 4.6 25.2 1.0
OD1 A:ASP802 4.7 30.4 1.0
N A:ASN806 4.8 32.5 1.0
C A:SER807 4.9 32.1 1.0
O A:HOH1328 5.0 36.2 1.0

Sodium binding site 2 out of 2 in 7g47

Go back to Sodium Binding Sites List in 7g47
Sodium binding site 2 out of 2 in the Crystal Structure of Rat Autotaxin in Complex with 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-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 3-[4- (Cyclopropylmethoxy)Naphthalen-2-Yl]-4-Methyl-1H-1,2,4-Triazol-5-One within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na905

b:16.2
occ:1.00
 O A:HOH1323 2.1 31.9 1.0
O A:ASP672 2.1 27.8 1.0
O A:TYR669 2.2 30.3 1.0
O A:HOH1356 2.3 36.6 1.0
O A:HOH1241 2.3 29.1 1.0
O A:MET675 2.3 23.6 1.0
C A:ASP672 3.4 30.2 1.0
C A:TYR669 3.4 29.6 1.0
C A:MET675 3.5 27.3 1.0
N A:MET675 4.1 30.6 1.0
O A:HOH1346 4.2 39.2 1.0
CA A:TYR669 4.2 26.2 1.0
CA A:LYS673 4.2 33.1 1.0
N A:LYS673 4.3 31.0 1.0
O A:LYS670 4.3 36.8 1.0
CA A:ASP672 4.3 29.2 1.0
N A:SER676 4.4 23.3 1.0
CA A:MET675 4.4 27.0 1.0
C A:LYS673 4.4 31.8 1.0
N A:LYS670 4.4 32.7 1.0
CA A:SER676 4.4 22.7 1.0
N A:ASP672 4.5 32.8 1.0
CB A:ASP672 4.5 30.2 1.0
O A:LYS673 4.6 34.0 1.0
CA A:LYS670 4.6 35.8 1.0
C A:LYS670 4.6 34.4 1.0
CB A:TYR669 4.6 25.6 1.0
N A:GLN674 4.8 31.3 1.0
C A:GLN674 4.9 32.5 1.0
CB A:SER676 4.9 23.7 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 23:17:21 2025

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