Sodium in PDB 7qbs: B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound.

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound., PDB code: 7qbs was solved by N.Bernardo-Garcia, 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)	45.00 / 2.33
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	119.29, 119.29, 68.56, 90, 90, 120
R / Rfree (%)	18.2 / 23.5

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. also contains other interesting chemical elements:

Iron	(Fe)	5 atoms
Cobalt	(Co)	1 atom

The binding sites of Sodium atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound. (pdb code 7qbs). 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 B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide Bound., PDB code: 7qbs:

Sodium binding site 1 out of 1 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, S-Adenosyl-L-Methionine, and Peptide 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, S-Adenosyl-L-Methionine, and Peptide Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:51.4 occ:1.00 O A:PHE121 2.3 57.3 1.0 OG A:SER162 2.4 53.3 1.0 O A:HOH669 2.4 62.7 1.0 O A:GLY118 2.8 54.2 1.0 OD1 A:ASP156 2.9 54.0 1.0 O A:GLU158 3.1 51.4 1.0 C A:PHE121 3.5 57.4 1.0 CB A:SER162 3.7 51.3 1.0 CG A:ASP156 3.8 53.4 1.0 C A:GLY118 3.9 53.6 1.0 C A:GLU158 3.9 51.0 1.0 N A:SER162 4.0 50.5 1.0 OD2 A:ASP156 4.0 53.1 1.0 CB A:GLU158 4.0 51.9 1.0 CA A:LYS119 4.0 52.3 1.0 O A:LYS119 4.1 53.4 1.0 CA A:SER162 4.1 50.5 1.0 C A:LYS119 4.1 52.9 1.0 N A:PHE121 4.3 55.0 1.0 CA A:PHE121 4.3 56.1 1.0 CA A:GLU158 4.4 50.7 1.0 N A:SER122 4.4 57.9 1.0 N A:GLU158 4.4 51.0 1.0 CA A:SER122 4.4 58.8 1.0 N A:LYS119 4.4 52.6 1.0 CB A:PHE121 4.5 56.0 1.0 CB A:ALA161 4.6 50.6 1.0 OG A:SER122 4.7 65.3 1.0 C A:ALA161 4.8 51.1 1.0 N A:PRO159 4.9 50.8 1.0 N A:GLY120 4.9 53.0 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