Sodium in PDB 7qbu: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbu was solved by C.D.Fyfe, L.M.G.Chavas, P.Legrand, A.Benjdia, O.Berteau, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	44.84 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	77.779, 79.493, 151.659, 90, 90, 90
R / Rfree (%)	19.1 / 22.5

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. also contains other interesting chemical elements:

Iron	(Fe)	10 atoms
Cobalt	(Co)	2 atoms

The binding sites of Sodium atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. (pdb code 7qbu). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound., PDB code: 7qbu:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:41.6 occ:1.00 OG A:SER162 2.2 43.9 1.0 O A:HOH702 2.3 43.8 1.0 O A:GLY118 2.4 41.6 1.0 O A:PHE121 2.6 44.6 1.0 OD1 A:ASP156 2.6 49.2 1.0 O A:GLU158 2.7 47.0 1.0 C A:GLY118 3.5 40.2 1.0 CG A:ASP156 3.5 46.7 1.0 C A:GLU158 3.5 47.3 1.0 OD2 A:ASP156 3.6 46.3 1.0 CB A:SER162 3.6 41.6 1.0 C A:PHE121 3.6 44.0 1.0 N A:SER162 3.9 41.6 1.0 CB A:GLU158 4.0 51.5 1.0 N A:GLU158 4.0 48.0 1.0 CA A:GLU158 4.0 48.2 1.0 CA A:LYS119 4.0 40.0 1.0 CA A:SER162 4.1 41.4 1.0 N A:PHE121 4.1 41.4 1.0 N A:LYS119 4.1 39.6 1.0 C A:LYS119 4.2 41.0 1.0 CA A:PHE121 4.3 42.3 1.0 O A:LYS119 4.3 41.9 1.0 CB A:PHE121 4.4 41.2 1.0 N A:PRO159 4.5 46.3 1.0 CA A:GLY118 4.5 39.4 1.0 N A:SER122 4.5 44.6 1.0 CA A:SER122 4.7 46.6 1.0 N A:GLY120 4.7 40.6 1.0 CA A:PRO159 4.8 45.9 1.0 CB A:ALA161 4.8 42.4 1.0 C A:ALA161 4.9 42.8 1.0 CB A:ASP156 4.9 45.1 1.0

Sodium binding site 2 out of 2 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Methyl-5'-Thioadenosine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:42.8 occ:1.00 O B:HOH706 2.2 40.1 1.0 OG B:SER162 2.4 40.6 1.0 O B:PHE121 2.5 46.6 1.0 O B:GLY118 2.5 46.2 1.0 O B:GLU158 2.7 44.1 1.0 OD1 B:ASP156 2.8 51.9 1.0 C B:PHE121 3.4 47.5 1.0 C B:GLU158 3.5 44.8 1.0 C B:GLY118 3.6 45.3 1.0 CG B:ASP156 3.6 50.3 1.0 CB B:SER162 3.7 39.7 1.0 OD2 B:ASP156 3.8 51.6 1.0 CB B:GLU158 3.8 49.4 1.0 CA B:GLU158 3.9 46.0 1.0 N B:GLU158 3.9 46.2 1.0 N B:SER162 4.0 40.2 1.0 N B:PHE121 4.0 46.3 1.0 CA B:LYS119 4.1 44.8 1.0 CA B:PHE121 4.2 46.5 1.0 CA B:SER162 4.2 39.9 1.0 C B:LYS119 4.2 46.0 1.0 N B:LYS119 4.3 44.9 1.0 N B:SER122 4.3 49.3 1.0 O B:LYS119 4.3 46.9 1.0 CB B:PHE121 4.3 45.7 1.0 CA B:SER122 4.5 51.8 1.0 N B:PRO159 4.6 44.1 1.0 CA B:GLY118 4.6 44.6 1.0 CB B:ALA161 4.7 41.7 1.0 N B:GLY120 4.8 46.0 1.0 C B:ALA161 4.9 41.1 1.0 CA B:PRO159 4.9 44.3 1.0 CG B:GLU158 5.0 57.1 1.0

C.D.Fyfe, N.Bernardo-Garcia, L.Fradale, S.Grimaldi, A.Guillot, C.Brewee, L.M.G.Chavas, P.Legrand, A.Benjdia, O.Berteau. Crystallographic Snapshots of A B 12 -Dependent Radical Sam Methyltransferase. Nature V. 602 336 2022.
ISSN: ESSN 1476-4687
PubMed: 35110733
DOI: 10.1038/S41586-021-04355-9