Sodium in PDB 7mjz: The Structure of Miab with Pentasulfide Bridge

All present enzymatic activity of The Structure of Miab with Pentasulfide Bridge:
2.8.4.3;

The structure of The Structure of Miab with Pentasulfide Bridge, PDB code: 7mjz was solved by O.A.Esakova, T.L.Grove, N.H.Yennawar, A.J.Arcinas, B.Wang, C.Krebs, S.C.Almo, S.J.Booker, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.68 / 2.08
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.215, 81.125, 118.326, 90, 90, 90
R / Rfree (%)	18.2 / 22.1

The structure of The Structure of Miab with Pentasulfide Bridge also contains other interesting chemical elements:

Iron

(Fe)

8 atoms

The binding sites of Sodium atom in the The Structure of Miab with Pentasulfide Bridge (pdb code 7mjz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the The Structure of Miab with Pentasulfide Bridge, PDB code: 7mjz:

Sodium binding site 1 out of 1 in the The Structure of Miab with Pentasulfide Bridge


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of The Structure of Miab with Pentasulfide Bridge within 5.0Å range: probe atom residue distance (Å) B Occ A:Na504 b:22.8 occ:1.00 O A:HOH638 2.3 24.2 1.0 O A:MET269 2.4 26.2 0.6 O A:ILE266 2.4 29.8 1.0 O A:MET269 2.4 26.2 0.4 O A:HOH776 2.4 36.6 1.0 O A:VAL272 2.6 22.0 1.0 C A:MET269 3.4 28.1 0.6 C A:MET269 3.5 28.1 0.4 C A:ILE266 3.6 27.0 1.0 C A:VAL272 3.7 21.1 1.0 CA A:PRO270 3.9 26.6 1.0 C A:PRO270 4.0 27.6 1.0 O A:PRO270 4.1 29.1 1.0 N A:PRO270 4.1 28.6 1.0 OE2 A:GLU420 4.1 25.2 1.0 CE A:LYS274 4.1 32.5 1.0 N A:VAL272 4.2 23.5 1.0 CG A:LYS274 4.2 20.9 1.0 CA A:VAL272 4.3 23.1 1.0 CA A:ILE266 4.4 24.3 1.0 N A:MET269 4.4 28.2 0.6 N A:MET269 4.4 28.4 0.4 O A:ALA267 4.4 26.6 1.0 CB A:VAL272 4.5 22.7 1.0 CA A:MET269 4.5 30.1 0.6 CG2 A:ILE266 4.5 21.4 1.0 C A:ALA267 4.5 28.5 1.0 CA A:MET269 4.5 30.1 0.4 N A:ALA267 4.6 26.6 1.0 CA A:ALA267 4.7 28.3 1.0 N A:ASN271 4.7 24.2 1.0 N A:CYS273 4.8 20.1 1.0 CD A:LYS274 4.8 23.6 1.0 N A:LYS274 4.9 20.9 1.0 C A:CYS273 4.9 23.0 1.0 O A:HOH718 5.0 31.8 1.0 O A:VAL265 5.0 27.8 1.0 CA A:CYS273 5.0 21.4 1.0

O.A.Esakova, T.L.Grove, N.H.Yennawar, A.J.Arcinas, B.Wang, C.Krebs, S.C.Almo, S.J.Booker. Structural Basis For Trna Methylthiolation By the Radical Sam Enzyme Miab Nature 2021.
ISSN: ESSN 1476-4687
DOI: 10.1038/S41586-021-03904-6