Magnesium in PDB 7mjv: Miab in the Complex with S-Adenosylmethionine and Rna

All present enzymatic activity of Miab in the Complex with S-Adenosylmethionine and Rna:
2.8.4.3;

The structure of Miab in the Complex with S-Adenosylmethionine and Rna, PDB code: 7mjv 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)	45.51 / 2.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	54.155, 81.442, 109.751, 90, 90, 90
R / Rfree (%)	24.3 / 27.3

The structure of Miab in the Complex with S-Adenosylmethionine and Rna also contains other interesting chemical elements:

Iron

(Fe)

7 atoms

The binding sites of Magnesium atom in the Miab in the Complex with S-Adenosylmethionine and Rna (pdb code 7mjv). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Miab in the Complex with S-Adenosylmethionine and Rna, PDB code: 7mjv:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg504 b:41.0 occ:1.00 O A:ILE266 2.3 45.5 1.0 O A:VAL272 2.3 34.9 1.0 O A:HOH617 2.3 50.1 1.0 O A:MET269 2.3 43.5 1.0 C A:VAL272 3.4 34.8 1.0 C A:ILE266 3.4 39.8 1.0 C A:MET269 3.5 49.2 1.0 OE2 A:GLU420 3.6 65.4 1.0 N A:VAL272 3.9 36.6 1.0 CA A:PRO270 4.0 39.6 1.0 CA A:VAL272 4.0 35.4 1.0 C A:PRO270 4.1 39.3 1.0 CB A:VAL272 4.1 39.3 1.0 O A:PRO270 4.1 44.2 1.0 CA A:ILE266 4.1 39.4 1.0 N A:PRO270 4.2 43.4 1.0 CG2 A:ILE266 4.2 36.6 1.0 CG A:LYS274 4.2 48.0 1.0 CE A:LYS274 4.4 51.7 1.0 N A:MET269 4.5 55.6 1.0 N A:ALA267 4.5 41.9 1.0 CA A:MET269 4.5 42.1 1.0 N A:CYS273 4.5 35.4 1.0 C A:ALA267 4.6 49.8 1.0 O A:ALA267 4.7 48.9 1.0 N A:ASN271 4.7 42.5 1.0 CA A:ALA267 4.7 41.4 1.0 O A:VAL265 4.8 42.6 1.0 CG1 A:VAL272 4.8 34.6 1.0 C A:CYS273 4.8 40.8 1.0 CB A:ILE266 4.8 38.4 1.0 CA A:CYS273 4.8 42.6 1.0 N A:LYS274 4.8 41.9 1.0 CD A:GLU420 4.9 63.0 1.0 C A:ASN271 4.9 37.2 1.0 CD A:LYS274 5.0 52.1 1.0

Magnesium binding site 2 out of 2 in the Miab in the Complex with S-Adenosylmethionine and Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Miab in the Complex with S-Adenosylmethionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:65.7 occ:1.00 O A:HOH603 2.4 46.0 1.0 N A:LYS351 2.9 42.7 1.0 O2' E:A38 3.3 51.4 1.0 O A:LYS351 3.6 43.3 1.0 CB A:LYS351 3.6 46.1 1.0 O3' E:A38 3.7 69.9 1.0 CA A:LYS351 3.8 48.2 1.0 CA A:PHE350 3.8 40.3 1.0 C A:PHE350 3.8 41.2 1.0 CB A:PHE350 3.8 39.7 1.0 CD A:ARG66 4.0 48.1 1.0 CG A:LYS351 4.0 50.7 1.0 C A:LYS351 4.1 47.5 1.0 CE A:LYS351 4.4 55.8 1.0 OP1 E:U39 4.4 64.6 1.0 CD1 A:PHE350 4.5 42.2 1.0 C2' E:A38 4.5 58.8 1.0 NE A:ARG66 4.6 52.8 1.0 C3' E:A38 4.6 65.0 1.0 CG A:PHE350 4.7 38.7 1.0 P E:U39 4.7 60.6 1.0 C4' E:A38 4.8 63.6 1.0 C5' E:U39 4.8 61.5 1.0 CD A:LYS351 4.9 51.5 1.0 OP1 E:A38 4.9 62.8 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