Sodium in PDB 8u42: Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis

The structure of Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis, PDB code: 8u42 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)	57.71 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	108.22, 115.41, 121.71, 90, 90, 90
R / Rfree (%)	18.3 / 20.9

The structure of Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis (pdb code 8u42). 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 From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis, PDB code: 8u42:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:13.1 occ:1.00 O A:MET375 2.6 23.4 1.0 O A:GLY377 2.6 22.7 1.0 O A:VAL379 2.7 21.7 1.0 OE2 A:GLU381 2.7 27.4 1.0 O A:GLN374 2.7 25.4 1.0 C A:MET375 3.3 25.6 1.0 CD A:GLU381 3.6 23.4 1.0 CG A:GLU381 3.7 19.4 1.0 C A:GLY377 3.8 21.4 1.0 C A:GLN374 3.8 24.9 1.0 C A:VAL379 3.9 20.2 1.0 CA A:MET375 3.9 21.5 1.0 N A:GLY377 4.0 18.4 1.0 C A:LEU376 4.0 22.4 1.0 N A:VAL379 4.1 23.4 1.0 N A:LEU376 4.1 24.7 1.0 O A:GLY415 4.2 26.8 1.0 CA A:LEU376 4.3 23.6 1.0 CA A:GLY414 4.4 19.9 1.0 O A:LYS413 4.4 20.4 1.0 N A:MET375 4.4 20.8 1.0 O A:LEU376 4.5 25.6 1.0 CA A:GLY377 4.5 18.9 1.0 C A:GLY414 4.5 22.2 1.0 CG2 A:VAL379 4.5 20.7 1.0 O A:GLY414 4.6 27.0 1.0 CA A:VAL379 4.6 17.9 1.0 NH2 A:ARG444 4.7 24.0 1.0 CZ2 A:TRP321 4.7 21.5 1.0 OE1 A:GLU381 4.7 27.1 1.0 N A:THR378 4.8 21.0 1.0 CD2 A:LEU218 4.9 19.7 1.0 N A:TRP380 4.9 20.2 1.0 CB A:THR378 4.9 25.4 1.0

Sodium binding site 2 out of 2 in the Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Ovsa From Halomonas Utahensis, A Selenoxide Synthase Involved in Ovoselenol Biosynthesis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:23.0 occ:1.00 OE2 B:GLU381 2.4 36.5 1.0 O B:MET375 2.7 36.3 1.0 O B:GLN374 2.7 39.5 1.0 O B:VAL379 2.7 34.1 1.0 O B:GLY377 2.7 31.6 1.0 C B:MET375 3.3 36.1 1.0 CD B:GLU381 3.5 33.2 1.0 CG B:GLU381 3.8 28.2 1.0 C B:GLN374 3.9 47.3 1.0 C B:GLY377 3.9 33.1 1.0 C B:VAL379 3.9 33.6 1.0 CA B:MET375 3.9 35.9 1.0 N B:GLY377 4.0 34.3 1.0 N B:LEU376 4.1 37.0 1.0 N B:VAL379 4.1 33.2 1.0 C B:LEU376 4.1 36.0 1.0 O B:GLY415 4.2 32.3 1.0 CA B:LEU376 4.3 34.8 1.0 CA B:GLY414 4.3 32.7 1.0 C B:GLY414 4.4 31.8 1.0 N B:MET375 4.4 39.1 1.0 O B:LYS413 4.4 30.1 1.0 CG2 B:VAL379 4.5 32.6 1.0 CA B:GLY377 4.5 31.5 1.0 O B:LEU376 4.5 39.7 1.0 O B:GLY414 4.5 34.9 1.0 CA B:VAL379 4.6 31.6 1.0 OE1 B:GLU381 4.6 31.7 1.0 NH2 B:ARG444 4.7 31.7 1.0 CZ2 B:TRP321 4.7 27.1 1.0 CD2 B:LEU218 4.8 32.0 1.0 N B:TRP380 4.9 32.3 1.0 N B:GLY415 5.0 33.2 1.0 N B:THR378 5.0 37.0 1.0 CB B:GLU381 5.0 28.4 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