Cobalt in PDB 7qbt: 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: 7qbt 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)	44.71 / 1.90
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	156.064, 163.915, 77.805, 90, 90, 90
R / Rfree (%)	20.3 / 22.9

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:

Sodium	(Na)	4 atoms
Iron	(Fe)	20 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 7qbt). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 4 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: 7qbt:
Jump to Cobalt binding site number: 1; 2; 3; 4;

Cobalt binding site 1 out of 4 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:26.6 occ:1.00 CO A:COB504 0.0 26.6 1.0 N21 A:COB504 1.8 26.2 1.0 N24 A:COB504 1.9 26.8 1.0 N22 A:COB504 1.9 26.5 1.0 N23 A:COB504 1.9 27.1 1.0 C1A A:COB504 2.0 27.2 1.0 C19 A:COB504 2.7 27.8 1.0 C9 A:COB504 2.8 26.8 1.0 C4 A:COB504 2.8 25.9 1.0 C11 A:COB504 2.8 27.1 1.0 C1 A:COB504 2.8 26.8 1.0 C6 A:COB504 2.9 26.4 1.0 C14 A:COB504 2.9 26.4 1.0 C16 A:COB504 2.9 26.6 1.0 C10 A:COB504 3.2 26.9 1.0 C5 A:COB504 3.3 25.9 1.0 C15 A:COB504 3.4 25.9 1.0 C20 A:COB504 3.5 24.6 1.0 CD1 A:LEU322 3.9 26.1 1.0 C2 A:COB504 4.1 27.5 1.0 C8 A:COB504 4.1 26.6 1.0 C3 A:COB504 4.1 26.6 1.0 C18 A:COB504 4.1 28.1 1.0 C17 A:COB504 4.2 26.6 1.0 C12 A:COB504 4.2 27.2 1.0 C7 A:COB504 4.2 26.7 1.0 C13 A:COB504 4.3 27.3 1.0 O A:HOH880 4.4 37.3 1.0 CD2 A:LEU322 4.4 26.5 1.0 C26 A:COB504 4.5 29.7 1.0 N40 A:COB504 4.6 25.6 1.0 CG A:LEU322 4.6 26.3 1.0 OH A:TYR23 4.8 41.5 1.0 C35 A:COB504 4.8 25.9 1.0 C53 A:COB504 4.9 25.6 1.0 C54 A:COB504 4.9 25.6 1.0

Cobalt binding site 2 out of 4 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:27.1 occ:1.00 CO B:COB504 0.0 27.1 1.0 N21 B:COB504 1.8 27.4 1.0 N24 B:COB504 1.9 26.9 1.0 N22 B:COB504 1.9 28.6 1.0 N23 B:COB504 1.9 27.7 1.0 C1A B:COB504 2.0 28.0 1.0 C19 B:COB504 2.7 27.4 1.0 C9 B:COB504 2.8 28.6 1.0 C4 B:COB504 2.8 27.6 1.0 C11 B:COB504 2.9 27.5 1.0 C1 B:COB504 2.9 26.8 1.0 C14 B:COB504 2.9 27.6 1.0 C6 B:COB504 2.9 28.6 1.0 C16 B:COB504 2.9 26.6 1.0 C10 B:COB504 3.2 27.9 1.0 C5 B:COB504 3.3 28.1 1.0 C15 B:COB504 3.3 26.9 1.0 C20 B:COB504 3.5 24.1 1.0 CD1 B:LEU322 3.9 25.6 1.0 C2 B:COB504 4.1 27.9 1.0 C8 B:COB504 4.1 29.3 1.0 C3 B:COB504 4.1 27.5 1.0 C18 B:COB504 4.2 27.2 1.0 C17 B:COB504 4.2 26.1 1.0 C7 B:COB504 4.2 29.6 1.0 C12 B:COB504 4.2 27.9 1.0 C13 B:COB504 4.2 28.1 1.0 CD2 B:LEU322 4.4 27.0 1.0 O B:HOH853 4.5 41.1 1.0 C26 B:COB504 4.5 30.1 1.0 CG B:LEU322 4.6 26.4 1.0 N40 B:COB504 4.6 32.0 1.0 C35 B:COB504 4.8 27.9 1.0 C53 B:COB504 4.8 26.2 1.0 OH B:TYR23 4.8 38.5 1.0 C54 B:COB504 4.9 24.8 1.0

Cobalt binding site 3 out of 4 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 3 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 C:Co504 b:32.7 occ:1.00 CO C:COB504 0.0 32.7 1.0 N21 C:COB504 1.8 33.0 1.0 N24 C:COB504 1.9 32.8 1.0 N22 C:COB504 1.9 33.4 1.0 N23 C:COB504 1.9 33.9 1.0 C1A C:COB504 2.0 32.7 1.0 C19 C:COB504 2.7 33.7 1.0 C9 C:COB504 2.8 33.6 1.0 C4 C:COB504 2.8 33.0 1.0 C11 C:COB504 2.8 34.0 1.0 C1 C:COB504 2.8 33.2 1.0 C14 C:COB504 2.9 34.2 1.0 C6 C:COB504 2.9 33.4 1.0 C16 C:COB504 2.9 32.9 1.0 C10 C:COB504 3.2 33.6 1.0 C5 C:COB504 3.3 32.8 1.0 C15 C:COB504 3.3 33.5 1.0 C20 C:COB504 3.5 32.4 1.0 CD1 C:LEU322 4.0 36.8 1.0 C2 C:COB504 4.1 33.4 1.0 C8 C:COB504 4.1 34.2 1.0 C18 C:COB504 4.1 34.0 1.0 C3 C:COB504 4.1 32.6 1.0 C17 C:COB504 4.2 32.6 1.0 C7 C:COB504 4.2 34.4 1.0 C13 C:COB504 4.2 34.5 1.0 C12 C:COB504 4.2 34.4 1.0 CD2 C:LEU322 4.5 37.7 1.0 C26 C:COB504 4.5 34.8 1.0 N40 C:COB504 4.6 34.7 1.0 O C:HOH767 4.6 47.6 1.0 CG C:LEU322 4.6 36.8 1.0 OH C:TYR23 4.8 47.2 1.0 C35 C:COB504 4.8 31.9 1.0 C54 C:COB504 4.8 31.9 1.0 C53 C:COB504 4.8 32.9 1.0

Cobalt binding site 4 out of 4 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 4 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 D:Co504 b:26.6 occ:1.00 CO D:COB504 0.0 26.6 1.0 N22 D:COB504 1.9 26.7 1.0 N21 D:COB504 1.9 26.9 1.0 N23 D:COB504 1.9 27.0 1.0 N24 D:COB504 1.9 26.9 1.0 C1A D:COB504 2.0 26.8 1.0 C19 D:COB504 2.8 27.6 1.0 C9 D:COB504 2.8 26.6 1.0 C11 D:COB504 2.8 27.1 1.0 C4 D:COB504 2.8 26.9 1.0 C1 D:COB504 2.9 26.8 1.0 C14 D:COB504 2.9 27.0 1.0 C6 D:COB504 2.9 26.8 1.0 C16 D:COB504 2.9 27.1 1.0 C10 D:COB504 3.1 26.8 1.0 C5 D:COB504 3.3 26.9 1.0 C15 D:COB504 3.3 27.2 1.0 C20 D:COB504 3.5 24.8 1.0 CD1 D:LEU322 4.0 26.8 1.0 C2 D:COB504 4.1 27.9 1.0 C8 D:COB504 4.1 26.4 1.0 C3 D:COB504 4.2 26.7 1.0 C18 D:COB504 4.2 28.0 1.0 C12 D:COB504 4.2 27.6 1.0 C7 D:COB504 4.2 26.6 1.0 C13 D:COB504 4.2 27.1 1.0 C17 D:COB504 4.2 27.1 1.0 CD2 D:LEU322 4.4 28.4 1.0 O D:HOH874 4.5 41.7 1.0 N40 D:COB504 4.5 26.9 1.0 C26 D:COB504 4.5 30.2 1.0 CG D:LEU322 4.7 27.5 1.0 C35 D:COB504 4.8 27.6 1.0 C53 D:COB504 4.9 27.2 1.0 OH D:TYR23 4.9 41.1 1.0 C54 D:COB504 4.9 25.4 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