Sodium in PDB 7mjx: Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna

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

The structure of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna, PDB code: 7mjx 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)	41.02 / 1.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.69, 97.12, 80.606, 90, 108.1, 90
R / Rfree (%)	14.9 / 17

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

Iron

(Fe)

14 atoms

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

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:12.5 occ:1.00 O A:ILE266 2.3 11.6 1.0 O A:MET269 2.3 10.2 1.0 O A:VAL272 2.3 9.9 1.0 O A:HOH807 2.3 12.6 1.0 O A:HOH803 2.5 16.8 1.0 C A:MET269 3.3 10.1 1.0 C A:VAL272 3.5 10.4 1.0 C A:ILE266 3.5 10.9 1.0 CA A:PRO270 3.9 10.8 1.0 N A:VAL272 4.0 9.7 1.0 N A:PRO270 4.0 10.6 1.0 CA A:VAL272 4.1 9.2 1.0 CG A:LYS274 4.1 11.5 1.0 C A:PRO270 4.1 11.2 1.0 CB A:VAL272 4.1 9.0 1.0 N A:MET269 4.2 12.0 1.0 O A:PRO270 4.2 13.7 1.0 CA A:MET269 4.3 13.1 0.4 CA A:MET269 4.3 13.1 0.6 CA A:ILE266 4.3 8.8 1.0 O A:HOH1165 4.3 28.6 1.0 O A:ALA267 4.4 13.1 1.0 C A:ALA267 4.4 10.0 1.0 CG2 A:ILE266 4.5 11.2 1.0 N A:ALA267 4.5 9.3 1.0 CA A:ALA267 4.6 9.8 1.0 OE2 A:GLU420 4.6 12.2 1.0 N A:CYS273 4.6 10.6 1.0 N A:ASN271 4.7 10.5 1.0 CD A:LYS274 4.7 16.4 1.0 C A:CYS273 4.8 9.1 1.0 CG1 A:VAL272 4.8 10.6 1.0 CB A:MET269 4.8 13.8 0.6 N A:LYS274 4.9 9.4 1.0 CB A:MET269 4.9 13.9 0.4 O A:VAL265 4.9 10.1 1.0 CA A:CYS273 4.9 9.3 1.0 O A:HOH824 4.9 13.4 1.0 O A:HOH801 4.9 23.4 1.0 N A:ASP268 5.0 9.8 1.0 C A:ASN271 5.0 9.9 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:12.8 occ:1.00 O B:ILE266 2.3 12.8 1.0 O B:MET269 2.3 10.9 1.0 O B:VAL272 2.3 10.3 1.0 O B:HOH948 2.4 16.7 1.0 O B:HOH722 2.4 13.6 1.0 C B:MET269 3.4 11.2 1.0 C B:VAL272 3.5 10.2 1.0 C B:ILE266 3.5 12.3 1.0 CA B:PRO270 3.9 11.8 1.0 N B:VAL272 3.9 10.6 1.0 O B:PRO270 4.0 14.8 1.0 C B:PRO270 4.0 14.4 1.0 CA B:VAL272 4.1 10.2 1.0 N B:PRO270 4.1 12.6 1.0 CG B:LYS274 4.1 10.8 1.0 CB B:VAL272 4.2 10.0 1.0 N B:MET269 4.2 10.9 1.0 CA B:ILE266 4.2 11.3 1.0 CE B:LYS274 4.3 17.4 1.0 CA B:MET269 4.3 15.8 1.0 O B:ALA267 4.4 13.7 1.0 CG2 B:ILE266 4.4 11.4 1.0 C B:ALA267 4.4 14.3 1.0 OE2 B:GLU420 4.5 12.1 1.0 N B:ALA267 4.5 11.5 1.0 N B:CYS273 4.6 10.0 1.0 CA B:ALA267 4.6 12.4 1.0 O B:HOH1219 4.6 31.6 1.0 N B:ASN271 4.7 11.4 1.0 O B:VAL265 4.8 12.5 1.0 C B:CYS273 4.8 9.9 1.0 CD B:LYS274 4.8 11.3 1.0 N B:LYS274 4.8 10.2 1.0 CG1 B:VAL272 4.8 9.6 1.0 CB B:MET269 4.9 12.1 1.0 CA B:CYS273 4.9 10.1 1.0 C B:ASN271 4.9 10.8 1.0 N B:ASP268 5.0 11.0 1.0 O B:HOH790 5.0 27.4 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Miab in the Complex with 5'-Deoxyadenosine, Methionine and Rna within 5.0Å range: probe atom residue distance (Å) B Occ M:Na101 b:13.2 occ:1.00 O M:HOH234 2.3 15.0 1.0 O M:HOH254 2.3 16.6 1.0 O M:HOH259 2.4 19.4 1.0 O2' M:C32 2.4 11.6 1.0 O2 M:C32 2.5 11.0 1.0 N7 M:A31 2.6 11.8 1.0 C2 M:C32 3.4 8.4 1.0 C2' M:C32 3.5 12.4 1.0 C8 M:A31 3.5 12.8 1.0 C5 M:A31 3.6 10.2 1.0 C1' M:C32 3.7 9.2 1.0 O M:HOH239 3.8 20.6 1.0 N1 M:C32 3.8 10.0 1.0 N6 M:A31 3.8 11.7 1.0 O M:HOH206 4.1 35.2 1.0 C6 M:A31 4.1 11.8 1.0 C5' M:U33 4.2 11.3 1.0 OP2 M:A31 4.2 11.9 1.0 N3 M:C32 4.3 9.4 1.0 O3' M:C32 4.6 11.7 1.0 N7 M:G30 4.6 13.2 1.0 OP2 M:G34 4.6 16.2 1.0 O M:HOH230 4.7 28.4 1.0 C3' M:C32 4.7 11.2 1.0 N9 M:A31 4.7 11.4 1.0 N7 M:G34 4.8 14.2 1.0 C4 M:A31 4.8 11.3 1.0 O M:HOH225 4.8 30.7 1.0 O M:HOH277 4.8 32.5 1.0 C8 M:G30 4.8 14.4 1.0 OP2 M:G30 4.9 20.7 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