Magnesium in PDB 7mjw: Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna

All present enzymatic activity of Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna:
2.8.4.3;

The structure of Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna, PDB code: 7mjw 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)	39.08 / 1.40
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.9, 97.413, 80.738, 90, 108.08, 90
R / Rfree (%)	14.9 / 17.4

The structure of Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna also contains other interesting chemical elements:

Iron

(Fe)

14 atoms

The binding sites of Magnesium atom in the Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna (pdb code 7mjw). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna, PDB code: 7mjw:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg505 b:15.8 occ:1.00 O A:ILE266 2.3 14.0 1.0 O A:MET269 2.3 13.6 1.0 O A:VAL272 2.3 13.9 1.0 O A:HOH673 2.3 19.4 1.0 O A:HOH844 2.4 20.4 1.0 C A:MET269 3.4 13.5 1.0 C A:VAL272 3.5 12.3 1.0 C A:ILE266 3.5 12.3 1.0 CA A:PRO270 3.9 15.1 1.0 N A:VAL272 3.9 12.8 1.0 O A:PRO270 4.0 19.2 1.0 C A:PRO270 4.0 17.3 1.0 CA A:VAL272 4.1 12.3 1.0 N A:PRO270 4.1 14.8 1.0 CB A:VAL272 4.2 12.9 1.0 CG A:LYS274 4.2 15.8 1.0 CE A:LYS274 4.2 21.0 1.0 CA A:ILE266 4.2 14.6 1.0 N A:MET269 4.3 14.8 1.0 CA A:MET269 4.4 17.2 1.0 CG2 A:ILE266 4.4 14.3 1.0 O A:ALA267 4.4 17.0 1.0 OE2 A:GLU420 4.5 18.0 1.0 C A:ALA267 4.5 15.5 1.0 N A:ALA267 4.5 12.7 1.0 N A:CYS273 4.6 12.2 1.0 CA A:ALA267 4.6 15.7 1.0 N A:ASN271 4.7 13.8 1.0 O A:VAL265 4.8 14.2 1.0 C A:CYS273 4.8 12.0 1.0 CD A:LYS274 4.8 19.1 1.0 N A:LYS274 4.8 13.0 1.0 CA A:CYS273 4.8 12.3 1.0 CG1 A:VAL272 4.9 12.5 1.0 C A:ASN271 4.9 13.1 1.0 CB A:MET269 4.9 16.3 1.0 N A:ASP268 5.0 15.4 1.0

Magnesium binding site 2 out of 3 in the Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg505 b:15.1 occ:1.00 O B:ILE266 2.3 14.0 1.0 O B:MET269 2.3 11.9 1.0 O B:HOH712 2.3 19.3 1.0 O B:VAL272 2.4 12.2 1.0 O B:HOH760 2.5 22.1 1.0 C B:MET269 3.4 13.4 1.0 C B:VAL272 3.5 11.8 1.0 C B:ILE266 3.5 13.5 1.0 CA B:PRO270 3.9 13.0 1.0 N B:VAL272 4.0 11.6 1.0 CA B:VAL272 4.1 11.1 1.0 N B:PRO270 4.1 14.5 1.0 CB B:VAL272 4.1 10.8 1.0 C B:PRO270 4.1 14.8 1.0 CG B:LYS274 4.2 17.0 0.5 O B:PRO270 4.2 17.4 1.0 N B:MET269 4.2 16.3 1.0 CG B:LYS274 4.3 16.9 0.5 CA B:ILE266 4.3 12.1 1.0 CA B:MET269 4.3 15.8 0.3 CA B:MET269 4.4 15.8 0.7 O B:ALA267 4.4 17.1 1.0 C B:ALA267 4.4 13.4 1.0 CG2 B:ILE266 4.5 13.8 1.0 N B:ALA267 4.5 11.7 1.0 CE B:LYS274 4.5 18.6 0.5 OE2 B:GLU420 4.5 18.0 0.4 CA B:ALA267 4.5 13.2 1.0 OE2 B:GLU420 4.6 16.1 0.6 N B:CYS273 4.6 11.6 1.0 N B:ASN271 4.7 12.6 1.0 O B:HOH708 4.8 28.5 1.0 CD B:LYS274 4.8 16.4 0.5 C B:CYS273 4.8 11.0 1.0 CB B:MET269 4.8 14.4 0.3 CG1 B:VAL272 4.9 12.7 1.0 O B:VAL265 4.9 13.0 1.0 CB B:MET269 4.9 14.3 0.7 N B:LYS274 4.9 11.3 1.0 CA B:CYS273 4.9 11.2 1.0 N B:ASP268 4.9 13.8 1.0 CD B:LYS274 4.9 17.5 0.5 C B:ASN271 5.0 11.9 1.0

Magnesium binding site 3 out of 3 in the Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Methylated Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ G:Mg101 b:17.9 occ:1.00 O G:HOH246 2.3 19.9 1.0 O G:HOH250 2.3 19.8 1.0 O2' G:C32 2.4 14.3 1.0 O G:HOH257 2.4 20.8 1.0 O2 G:C32 2.5 14.2 1.0 N7 G:A31 2.7 13.2 1.0 C2 G:C32 3.4 13.9 1.0 C2' G:C32 3.5 13.3 1.0 C8 G:A31 3.6 14.4 1.0 C5 G:A31 3.7 12.2 1.0 C1' G:C32 3.7 11.9 1.0 O G:HOH235 3.7 26.2 1.0 N1 G:C32 3.8 12.8 1.0 N6 G:A31 3.9 13.7 1.0 C5' G:U33 4.2 15.9 1.0 C6 G:A31 4.2 12.2 1.0 OP2 G:A31 4.2 16.6 1.0 N3 G:C32 4.4 11.6 1.0 O G:HOH237 4.6 30.3 1.0 OP2 G:G34 4.6 19.1 1.0 O3' G:C32 4.6 14.0 1.0 N7 G:G30 4.7 16.8 1.0 C3' G:C32 4.7 16.4 1.0 O G:HOH232 4.7 33.9 1.0 N7 G:G34 4.8 20.3 1.0 N9 G:A31 4.8 14.2 1.0 C4 G:A31 4.8 13.2 1.0 C8 G:G30 4.9 16.1 1.0 O G:HOH269 4.9 32.4 1.0 OP2 G:G30 4.9 24.4 1.0 C4' G:U33 5.0 17.1 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