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

The structure of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv 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)	49.40 / 2.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	155.498, 163, 77.328, 90, 90, 90
R / Rfree (%)	21.4 / 23.5

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

Cobalt	(Co)	4 atoms
Iron	(Fe)	20 atoms

The binding sites of Sodium atom in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. (pdb code 7qbv). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:42.0 occ:1.00 OD1 A:ASP156 2.5 46.6 1.0 O A:PHE121 2.7 45.2 1.0 O A:GLU158 2.9 45.0 1.0 O A:GLY118 3.1 45.8 1.0 OG A:SER162 3.1 43.7 1.0 N A:GLU158 3.3 44.5 1.0 CB A:GLU158 3.4 48.7 1.0 C A:GLU158 3.4 44.8 1.0 C A:PHE121 3.5 45.2 1.0 O A:LYS119 3.5 45.5 1.0 CA A:GLU158 3.6 45.2 1.0 CG A:ASP156 3.7 46.1 1.0 C A:LYS119 3.8 45.4 1.0 CA A:LYS119 3.9 45.4 1.0 CD A:PRO157 4.1 42.6 1.0 CG A:PRO157 4.1 44.3 1.0 C A:GLY118 4.1 45.6 1.0 OD2 A:ASP156 4.2 47.4 1.0 CA A:SER122 4.2 45.9 1.0 N A:SER122 4.2 45.4 1.0 N A:PHE121 4.2 44.5 1.0 OG A:SER122 4.3 50.6 1.0 CG A:GLU158 4.4 57.4 1.0 N A:PRO157 4.4 43.1 1.0 CA A:PHE121 4.4 44.6 1.0 C A:PRO157 4.5 44.2 1.0 N A:PRO159 4.5 44.2 1.0 N A:LYS119 4.5 45.1 1.0 CB A:SER162 4.5 42.0 1.0 N A:GLY120 4.7 45.1 1.0 N A:SER162 4.8 41.2 1.0 C A:ASP156 4.8 43.3 1.0 CA A:PRO157 4.9 43.4 1.0 CB A:SER122 4.9 47.5 1.0 CB A:ASP156 4.9 43.6 1.0 CB A:PHE121 4.9 44.0 1.0 C A:GLY120 4.9 44.9 1.0

Sodium binding site 2 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na505 b:39.7 occ:1.00 OD1 B:ASP156 2.5 52.7 1.0 O B:PHE121 2.6 42.6 1.0 O B:GLY118 2.9 40.3 1.0 O B:GLU158 3.0 50.0 1.0 OG B:SER162 3.1 46.8 1.0 N B:GLU158 3.4 50.1 1.0 O B:LYS119 3.5 40.8 1.0 C B:PHE121 3.5 42.5 1.0 C B:GLU158 3.6 49.8 1.0 CB B:GLU158 3.6 53.9 1.0 CG B:ASP156 3.7 52.2 1.0 C B:LYS119 3.7 40.6 1.0 CA B:GLU158 3.7 50.5 1.0 CA B:LYS119 3.8 40.1 1.0 C B:GLY118 4.0 40.1 1.0 CD B:PRO157 4.1 49.1 1.0 N B:PHE121 4.1 40.9 1.0 OD2 B:ASP156 4.1 53.5 1.0 CG B:PRO157 4.1 50.7 1.0 N B:SER122 4.2 43.1 1.0 CA B:SER122 4.2 44.0 1.0 OG B:SER122 4.3 48.9 1.0 CA B:PHE121 4.3 41.4 1.0 N B:LYS119 4.4 39.8 1.0 N B:PRO157 4.5 49.8 1.0 CB B:SER162 4.5 45.0 1.0 CG B:GLU158 4.5 61.5 1.0 N B:GLY120 4.5 40.4 1.0 C B:PRO157 4.6 50.4 1.0 N B:PRO159 4.7 48.9 1.0 CB B:PHE121 4.8 40.9 1.0 C B:GLY120 4.8 40.9 1.0 N B:SER162 4.8 44.4 1.0 C B:ASP156 4.9 49.8 1.0 CB B:ASP156 4.9 49.7 1.0 CB B:SER122 4.9 45.8 1.0 CA B:PRO157 5.0 49.9 1.0

Sodium binding site 3 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ C:Na505 b:42.7 occ:1.00 OD1 C:ASP156 2.5 51.8 1.0 O C:PHE121 2.5 47.2 1.0 O C:GLY118 2.6 46.5 1.0 OG C:SER162 2.7 47.9 1.0 O C:GLU158 2.9 49.9 1.0 C C:PHE121 3.5 47.3 1.0 CG C:ASP156 3.6 51.8 1.0 C C:GLU158 3.6 49.9 1.0 O C:LYS119 3.7 47.0 1.0 N C:GLU158 3.7 50.3 1.0 C C:GLY118 3.7 46.5 1.0 CA C:LYS119 3.8 46.5 1.0 C C:LYS119 3.8 46.9 1.0 CB C:GLU158 3.8 53.6 1.0 CA C:GLU158 3.9 50.5 1.0 OD2 C:ASP156 3.9 53.2 1.0 N C:PHE121 4.1 46.6 1.0 CB C:SER162 4.1 46.3 1.0 N C:LYS119 4.2 46.3 1.0 CA C:PHE121 4.3 46.9 1.0 N C:SER122 4.3 47.7 1.0 CA C:SER122 4.4 48.3 1.0 CD C:PRO157 4.4 49.3 1.0 N C:SER162 4.5 45.8 1.0 CG C:PRO157 4.5 50.9 1.0 N C:GLY120 4.6 46.9 1.0 CB C:PHE121 4.6 46.5 1.0 N C:PRO159 4.6 49.2 1.0 OG C:SER122 4.6 52.6 1.0 N C:PRO157 4.7 50.0 1.0 CA C:SER162 4.7 45.4 1.0 CG C:GLU158 4.8 59.9 1.0 C C:GLY120 4.9 46.9 1.0 CB C:ASP156 4.9 50.0 1.0 C C:PRO157 4.9 50.5 1.0 CA C:GLY118 5.0 46.5 1.0

Sodium binding site 4 out of 4 in the B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of B12-Dependent Radical Sam Methyltransferase, MMP10 with [4FE-4S] Cluster, Cobalamin, and S-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ D:Na505 b:36.7 occ:1.00 O D:PHE121 2.4 54.7 1.0 OD1 D:ASP156 2.6 60.3 1.0 OG D:SER162 2.6 52.0 1.0 O D:GLY118 2.7 52.2 1.0 O D:GLU158 2.7 55.8 1.0 C D:PHE121 3.4 54.5 1.0 C D:GLU158 3.5 55.9 1.0 CG D:ASP156 3.7 60.0 1.0 CB D:GLU158 3.7 60.1 1.0 N D:GLU158 3.7 56.5 1.0 CA D:GLU158 3.8 56.8 1.0 C D:GLY118 3.8 51.8 1.0 O D:LYS119 3.8 52.6 1.0 CA D:LYS119 4.0 51.7 1.0 C D:LYS119 4.0 52.4 1.0 OD2 D:ASP156 4.0 61.4 1.0 CB D:SER162 4.0 50.7 1.0 N D:PHE121 4.1 53.3 1.0 N D:SER122 4.2 55.2 1.0 CA D:PHE121 4.2 53.6 1.0 CA D:SER122 4.3 56.4 1.0 N D:SER162 4.3 51.4 1.0 N D:LYS119 4.4 51.5 1.0 CB D:PHE121 4.5 52.9 1.0 CD D:PRO157 4.6 56.3 1.0 N D:PRO159 4.6 55.0 1.0 CA D:SER162 4.6 50.5 1.0 OG D:SER122 4.6 61.6 1.0 CG D:PRO157 4.7 57.9 1.0 N D:GLY120 4.7 52.4 1.0 CG D:GLU158 4.7 67.3 1.0 CB D:ALA161 4.8 53.0 1.0 N D:PRO157 4.8 56.8 1.0 C D:GLY120 4.9 53.6 1.0 C D:PRO157 4.9 56.9 1.0 CB D:ASP156 5.0 57.5 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