Cobalt 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
Sodium	(Na)	2 atoms

The binding sites of Cobalt 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 Cobalt atom.
In total 2 binding sites of Cobalt 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 Cobalt binding site number: 1; 2;

Cobalt 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 Cobalt with other atoms in the Co 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:Co504 b:36.7 occ:1.00 CO A:COB504 0.0 36.7 1.0 N21 A:COB504 1.8 36.9 1.0 N22 A:COB504 1.8 36.7 1.0 N23 A:COB504 1.9 36.2 1.0 N24 A:COB504 1.9 37.3 1.0 C1A A:COB504 2.0 36.8 1.0 C19 A:COB504 2.7 37.8 1.0 C9 A:COB504 2.7 36.6 1.0 C4 A:COB504 2.8 36.9 1.0 C11 A:COB504 2.8 36.3 1.0 C1 A:COB504 2.9 37.6 1.0 C6 A:COB504 2.9 37.2 1.0 C14 A:COB504 2.9 36.1 1.0 C16 A:COB504 2.9 37.5 1.0 C10 A:COB504 3.1 36.5 1.0 C5 A:COB504 3.2 37.2 1.0 C15 A:COB504 3.3 36.3 1.0 C20 A:COB504 3.6 36.8 1.0 C2 A:COB504 4.0 37.6 1.0 C8 A:COB504 4.1 36.8 1.0 CD1 A:LEU322 4.1 30.3 1.0 C3 A:COB504 4.1 36.9 1.0 C18 A:COB504 4.1 38.5 1.0 C12 A:COB504 4.2 36.3 1.0 C7 A:COB504 4.2 37.4 1.0 C13 A:COB504 4.2 36.0 1.0 C17 A:COB504 4.2 37.7 1.0 CD2 A:LEU322 4.4 31.7 1.0 C26 A:COB504 4.4 38.9 1.0 N40 A:COB504 4.5 39.1 1.0 CG A:LEU322 4.7 31.9 1.0 C35 A:COB504 4.7 37.5 1.0 CS A:MTA503 4.8 62.5 1.0 C53 A:COB504 4.9 35.6 1.0 C54 A:COB504 4.9 37.4 1.0

Cobalt 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 Cobalt with other atoms in the Co 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:Co504 b:36.1 occ:1.00 CO B:COB504 0.0 36.1 1.0 N21 B:COB504 1.8 36.9 1.0 N22 B:COB504 1.8 37.0 1.0 N23 B:COB504 1.9 36.3 1.0 N24 B:COB504 1.9 36.1 1.0 C1A B:COB504 2.0 36.1 1.0 C19 B:COB504 2.7 36.3 1.0 C9 B:COB504 2.7 36.9 1.0 C4 B:COB504 2.8 37.2 1.0 C11 B:COB504 2.8 36.2 1.0 C6 B:COB504 2.9 37.7 1.0 C1 B:COB504 2.9 36.6 1.0 C14 B:COB504 2.9 36.4 1.0 C16 B:COB504 3.0 36.5 1.0 C10 B:COB504 3.1 36.6 1.0 C5 B:COB504 3.2 37.4 1.0 C15 B:COB504 3.4 36.7 1.0 C20 B:COB504 3.6 35.4 1.0 C2 B:COB504 4.0 37.2 1.0 C8 B:COB504 4.1 37.0 1.0 C3 B:COB504 4.1 36.8 1.0 CD1 B:LEU322 4.1 31.0 1.0 C18 B:COB504 4.1 36.5 1.0 C7 B:COB504 4.2 38.2 1.0 C12 B:COB504 4.2 35.9 1.0 C13 B:COB504 4.2 35.8 1.0 C17 B:COB504 4.2 36.1 1.0 CD2 B:LEU322 4.4 32.9 1.0 C26 B:COB504 4.4 38.4 1.0 N40 B:COB504 4.5 39.4 1.0 CG B:LEU322 4.7 32.2 1.0 C35 B:COB504 4.7 37.1 1.0 C53 B:COB504 4.9 36.4 1.0 C54 B:COB504 4.9 35.4 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