Sodium in PDB 8u41: Ovsa From Halomonas Utahensis, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine

The structure of Ovsa From Halomonas Utahensis, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine, PDB code: 8u41 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)	69.34 / 2.72
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	160.129, 160.129, 122.312, 90, 90, 120
R / Rfree (%)	22.5 / 24.6

The structure of Ovsa From Halomonas Utahensis, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine also contains other interesting chemical elements:

Iron

(Fe)

2 atoms

The binding sites of Sodium atom in the Ovsa From Halomonas Utahensis, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine (pdb code 8u41). 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, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine, PDB code: 8u41:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Ovsa From Halomonas Utahensis, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine


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, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine within 5.0Å range: probe atom residue distance (Å) B Occ A:Na502 b:62.7 occ:1.00 O A:GLY377 2.0 76.9 1.0 O A:MET375 2.2 72.2 1.0 OE2 A:GLU381 2.2 68.9 1.0 O A:VAL379 3.1 77.1 1.0 C A:GLY377 3.1 70.6 1.0 N A:GLY377 3.3 88.8 1.0 O A:GLN374 3.3 88.6 1.0 C A:MET375 3.3 73.5 1.0 CD A:GLU381 3.4 67.1 1.0 N A:VAL379 3.8 66.0 1.0 CA A:GLY377 3.8 74.6 1.0 O A:GLY415 3.8 70.2 1.0 C A:VAL379 4.0 71.9 1.0 CA A:GLY414 4.0 68.5 1.0 CA A:MET375 4.1 77.7 1.0 CG A:GLU381 4.1 69.0 1.0 N A:THR378 4.2 58.3 1.0 C A:LEU376 4.2 81.5 1.0 C A:GLN374 4.3 79.2 1.0 CB A:THR378 4.3 80.2 1.0 N A:LEU376 4.4 68.1 1.0 OE1 A:GLU381 4.4 57.6 1.0 N A:GLY415 4.4 77.5 1.0 C A:GLY414 4.4 70.4 1.0 CA A:VAL379 4.5 65.9 1.0 CA A:THR378 4.6 61.5 1.0 O A:LYS413 4.6 65.7 1.0 C A:THR378 4.6 66.1 1.0 CA A:LEU376 4.6 81.7 1.0 N A:MET375 4.7 75.6 1.0 OG1 A:THR378 4.7 80.2 1.0 NH1 A:ARG444 4.8 75.6 1.0 CZ2 A:TRP321 4.8 61.2 1.0 C A:GLY415 4.9 71.7 1.0 CD1 A:LEU218 4.9 66.5 1.0 N A:GLU381 4.9 65.7 1.0 CB A:GLU381 4.9 69.8 1.0 CG2 A:VAL379 5.0 58.2 1.0

Sodium binding site 2 out of 2 in the Ovsa From Halomonas Utahensis, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine


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, An Ovoselenol-Biosynthetic Selenoxide Synthase in Complex with Histidine within 5.0Å range: probe atom residue distance (Å) B Occ B:Na502 b:57.0 occ:1.00 O B:MET375 2.4 68.0 1.0 O B:GLY377 2.5 73.3 1.0 OE2 B:GLU381 2.6 73.4 1.0 O B:GLN374 2.8 76.2 1.0 O B:VAL379 3.0 63.2 1.0 CG B:GLU381 3.3 64.5 1.0 CD B:GLU381 3.3 62.5 1.0 C B:MET375 3.3 68.8 1.0 C B:GLY377 3.7 65.1 1.0 N B:GLY377 3.8 76.6 1.0 C B:GLN374 3.9 70.3 1.0 O B:GLY415 3.9 72.1 1.0 N B:VAL379 4.0 74.9 1.0 CA B:MET375 4.0 65.6 1.0 C B:VAL379 4.1 65.8 1.0 N B:LEU376 4.4 74.7 1.0 CA B:GLY377 4.4 59.0 1.0 N B:MET375 4.4 68.3 1.0 CD1 B:LEU218 4.5 59.4 1.0 CA B:GLY414 4.5 75.9 1.0 C B:LEU376 4.5 69.0 1.0 CD2 B:LEU218 4.5 70.3 1.0 OE1 B:GLU381 4.5 52.1 1.0 CA B:LEU376 4.7 77.7 1.0 CA B:VAL379 4.7 70.5 1.0 CB B:THR378 4.7 70.4 1.0 O B:LYS413 4.7 65.4 1.0 CB B:GLU381 4.8 63.0 1.0 N B:THR378 4.8 61.2 1.0 CG2 B:VAL379 4.8 56.6 1.0 CZ2 B:TRP321 4.8 69.2 1.0 N B:GLY415 4.8 78.5 1.0 C B:GLY414 4.9 79.2 1.0 NH2 B:ARG444 4.9 59.7 1.0 N B:GLU381 4.9 56.9 1.0 C B:THR378 5.0 71.3 1.0 CG B:LEU218 5.0 62.2 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