Sodium in PDB 8ux5: Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity

The structure of Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity, PDB code: 8ux5 was solved by K.A.Ireland, K.M.Davis, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.09 / 3.06
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	162.174, 162.174, 124.663, 90, 90, 120
R / Rfree (%)	20.3 / 25.3

The structure of Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity (pdb code 8ux5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity, PDB code: 8ux5:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:65.6 occ:1.00 OE2 A:GLU381 2.1 93.4 1.0 O A:MET375 2.2 91.7 1.0 O A:GLY377 2.5 74.6 1.0 O A:VAL379 2.9 91.2 1.0 O A:GLN374 3.2 101.3 1.0 C A:MET375 3.3 98.7 1.0 CD A:GLU381 3.4 94.3 1.0 N A:GLY377 3.7 99.7 1.0 C A:GLY377 3.7 83.9 1.0 CA A:MET375 4.1 103.4 1.0 CG A:GLU381 4.1 82.2 1.0 C A:VAL379 4.1 96.3 1.0 N A:VAL379 4.1 82.9 1.0 O A:GLY415 4.2 84.6 1.0 CA A:GLY414 4.2 83.9 1.0 N A:GLY415 4.2 91.5 1.0 N A:LEU376 4.3 99.3 1.0 C A:GLN374 4.3 100.2 1.0 CA A:GLY377 4.3 81.3 1.0 OE1 A:GLU381 4.3 98.2 1.0 C A:LEU376 4.4 104.3 1.0 CA A:LEU376 4.5 104.4 1.0 N A:MET375 4.7 96.7 1.0 CA A:VAL379 4.7 99.3 1.0 C A:GLY414 4.7 83.8 1.0 CZ2 A:TRP321 4.8 82.4 1.0 O A:LYS413 4.8 89.1 1.0 N A:THR378 4.8 86.3 1.0 CB A:THR378 4.8 99.6 1.0 CB A:GLU381 4.9 87.8 1.0 C A:THR378 4.9 81.4 1.0 N A:GLU381 5.0 83.3 1.0

Sodium binding site 2 out of 2 in the Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ovsa M401Y/Q430N/A431F From Halomonas Utahensis, A Hercynine-Binding Variant with Selenoneine-Biosynthetic Activity within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:67.2 occ:1.00 O B:MET375 2.2 85.8 1.0 O B:GLY377 2.4 92.9 1.0 O B:VAL379 2.7 77.0 1.0 O B:GLN374 3.1 97.8 1.0 OE2 B:GLU381 3.2 90.5 1.0 C B:MET375 3.2 84.8 1.0 CG B:GLU381 3.6 88.2 1.0 C B:GLY377 3.6 78.6 1.0 N B:GLY377 3.7 86.2 1.0 C B:VAL379 3.8 82.2 1.0 CD B:GLU381 3.8 80.5 1.0 O B:GLY415 3.9 87.0 1.0 C B:LEU376 3.9 89.6 1.0 N B:LEU376 4.0 86.1 1.0 CA B:MET375 4.1 96.4 1.0 CA B:LEU376 4.1 98.9 1.0 C B:GLN374 4.2 97.2 1.0 N B:VAL379 4.2 92.3 1.0 CA B:GLY377 4.2 79.3 1.0 N B:GLY415 4.3 99.6 1.0 O B:LEU376 4.4 93.6 1.0 CA B:GLY414 4.5 94.7 1.0 CA B:VAL379 4.5 85.5 1.0 N B:MET375 4.6 90.0 1.0 N B:THR378 4.7 75.5 1.0 CG2 B:VAL379 4.7 67.6 1.0 C B:THR378 4.8 83.0 1.0 N B:TRP380 4.8 94.3 1.0 O B:LYS413 4.8 86.5 1.0 CZ2 B:TRP321 4.8 80.3 1.0 C B:GLY414 4.9 101.1 1.0 CB B:THR378 4.9 84.0 1.0 C B:GLY415 4.9 81.0 1.0 CD1 B:LEU218 4.9 73.0 1.0 N B:GLU381 4.9 78.1 1.0

C.M.Kayrouz, K.A.Ireland, V.Y.Ying, K.M.Davis, M.R.Seyedsayamdost. Discovery of the Selenium-Containing Antioxidant Ovoselenol Derived From Convergent Evolution Nat.Chem. 2024.
ISSN: ESSN 1755-4349