Sodium in PDB 6vue: Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol

All present enzymatic activity of Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol:
4.3.99.4;

The structure of Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol, PDB code: 6vue was solved by M.A.Ortega, C.L.Drennan, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.39 / 2.28
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	228.525, 228.525, 78.792, 90.00, 90.00, 90.00
R / Rfree (%)	16.4 / 19.7

The binding sites of Sodium atom in the Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol (pdb code 6vue). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol, PDB code: 6vue:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:24.9 occ:1.00 O A:MET748 2.3 22.9 1.0 O A:HOH1147 2.4 20.3 1.0 O A:SER746 2.4 20.4 1.0 O A:HOH1235 2.4 21.7 1.0 O B:HOH1205 2.5 24.4 1.0 O A:HOH1173 2.6 17.2 1.0 C A:SER746 3.4 23.7 1.0 C A:MET748 3.4 21.7 1.0 CA A:SER746 3.9 19.4 1.0 CA A:ALA749 4.0 19.8 1.0 N A:ALA749 4.1 18.9 1.0 ND2 A:ASN750 4.2 21.4 1.0 O A:LEU787 4.3 21.8 1.0 N A:MET748 4.3 21.6 1.0 N A:ASN750 4.4 19.5 1.0 C A:LYS747 4.4 21.9 1.0 O B:HOH1171 4.5 25.7 1.0 N A:LYS747 4.5 22.2 1.0 CA A:MET748 4.5 21.5 1.0 CB A:SER746 4.5 20.4 1.0 O A:VAL745 4.7 21.3 1.0 O A:GLY788 4.7 21.1 1.0 O A:LYS747 4.8 21.6 1.0 C A:ALA749 4.8 20.4 1.0 CA A:LYS747 4.8 22.3 1.0 OD1 A:ASN789 4.8 22.1 1.0

Sodium binding site 2 out of 2 in the Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Wild-Type Choline Tma Lyase in Complex with 1-Methyl-1,2,3,6- Tetrahydropyridin-3-Ol within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:21.7 occ:1.00 O B:MET748 2.2 21.5 1.0 O B:HOH1178 2.3 24.4 1.0 O B:HOH1200 2.3 26.4 1.0 O B:SER746 2.4 24.4 1.0 O B:HOH1017 2.6 23.1 1.0 O A:HOH1194 2.6 30.2 1.0 C B:SER746 3.3 25.4 1.0 C B:MET748 3.3 23.1 1.0 CA B:SER746 3.8 23.8 1.0 CA B:ALA749 4.0 20.7 1.0 N B:ALA749 4.0 20.6 1.0 ND2 B:ASN750 4.0 24.8 1.0 N B:MET748 4.1 22.4 1.0 C B:LYS747 4.2 25.0 1.0 N B:ASN750 4.3 24.1 1.0 O B:LEU787 4.3 23.2 1.0 CA B:MET748 4.3 22.7 1.0 N B:LYS747 4.4 24.0 1.0 CB B:SER746 4.5 25.2 1.0 O B:VAL745 4.5 26.8 1.0 O A:HOH1177 4.5 24.6 1.0 O B:LYS747 4.6 25.2 1.0 CA B:LYS747 4.6 24.4 1.0 C B:ALA749 4.7 22.4 1.0 O B:GLY788 4.8 23.3 1.0 OD1 B:ASN789 4.9 24.2 1.0 CG B:ASN750 5.0 23.6 1.0 N B:SER746 5.0 24.3 1.0

M.Bollenbach, M.Ortega, M.Orman, C.L.Drennan, E.P.Balskus. Discovery of A Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism By Human Gut Bacteria. Acs Med.Chem.Lett. V. 11 1980 2020.
ISSN: ISSN 1948-5875
PubMed: 33062182
DOI: 10.1021/ACSMEDCHEMLETT.0C00005