Sodium in PDB 8fbx: Selenosugar Synthase Senb From Variovorax Paradoxus

The structure of Selenosugar Synthase Senb From Variovorax Paradoxus, PDB code: 8fbx 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)	47.95 / 2.25
Space group	P 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	93, 68.56, 93.57, 90, 118.13, 90
R / Rfree (%)	20.2 / 23.8

The structure of Selenosugar Synthase Senb From Variovorax Paradoxus also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Selenosugar Synthase Senb From Variovorax Paradoxus (pdb code 8fbx). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Selenosugar Synthase Senb From Variovorax Paradoxus, PDB code: 8fbx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Selenosugar Synthase Senb From Variovorax Paradoxus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Selenosugar Synthase Senb From Variovorax Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:34.9 occ:1.00 O A:HOH625 2.5 44.5 1.0 O A:CYS35 2.5 36.2 1.0 O A:SER32 2.6 29.8 1.0 O A:HOH622 2.7 40.8 1.0 O A:HOH600 3.0 40.4 1.0 C A:CYS35 3.4 28.5 1.0 C A:SER32 3.6 31.9 1.0 CA A:SER32 3.8 33.2 1.0 CA A:SER36 3.9 35.0 1.0 N A:SER36 4.0 26.7 1.0 CB A:SER32 4.1 26.3 1.0 OG A:SER32 4.3 39.4 1.0 N A:CYS35 4.4 31.9 1.0 CA A:CYS35 4.5 33.1 1.0 N A:ALA37 4.5 28.9 1.0 C A:SER36 4.8 36.4 1.0 N A:PRO33 4.8 32.1 1.0 CB A:SER36 4.8 33.5 1.0

Sodium binding site 2 out of 2 in the Selenosugar Synthase Senb From Variovorax Paradoxus


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Selenosugar Synthase Senb From Variovorax Paradoxus within 5.0Å range: probe atom residue distance (Å) B Occ C:Na402 b:45.6 occ:1.00 O C:HOH523 2.4 48.5 1.0 O C:CYS200 2.5 41.6 1.0 O C:TYR203 2.5 36.1 1.0 O C:ALA197 2.7 39.2 1.0 O C:PRO201 2.8 44.1 1.0 C C:PRO201 3.2 39.2 1.0 CA C:PRO201 3.3 40.1 1.0 C C:CYS200 3.4 40.6 1.0 C C:ALA197 3.7 42.6 1.0 C C:TYR203 3.7 34.9 1.0 N C:PRO201 3.8 38.7 1.0 CA C:ALA197 4.0 39.6 1.0 N C:TYR203 4.0 29.7 1.0 N C:GLY202 4.2 37.9 1.0 CA C:TYR203 4.4 33.0 1.0 CB C:ALA197 4.4 36.0 1.0 C C:GLY202 4.6 34.1 1.0 CB C:PRO201 4.7 40.6 1.0 CA C:CYS200 4.7 38.1 1.0 N C:ARG204 4.7 30.9 1.0 CA C:GLY202 4.9 34.4 1.0 N C:SER198 4.9 42.9 1.0 N C:CYS200 5.0 40.0 1.0 CA C:ARG204 5.0 32.4 1.0

K.A.Ireland, C.M.Kayrouz, J.Huang, M.R.Seyedsayamdost, K.M.Davis. Structural Characterization and Ligand-Induced Conformational Changes of Senb, A Se-Glycosyltransferase Involved in Selenoneine Biosynthesis Biochemistry 2023.
ISSN: ISSN 0006-2960
DOI: 10.1021/ACS.BIOCHEM.3C00452