Cobalt 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:

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-Adenosyl-L-Homocysteine Bound. (pdb code 7qbv). 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-Adenosyl-L-Homocysteine Bound., PDB code: 7qbv:
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-Adenosyl-L-Homocysteine 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ A:Co504 b:40.0 occ:1.00 CO A:COB504 0.0 40.0 1.0 N21 A:COB504 1.8 40.2 1.0 N22 A:COB504 1.8 39.4 1.0 N23 A:COB504 1.9 40.1 1.0 N24 A:COB504 1.9 40.5 1.0 C1A A:COB504 2.0 40.3 1.0 C19 A:COB504 2.7 41.0 1.0 C9 A:COB504 2.8 39.3 1.0 C4 A:COB504 2.8 39.8 1.0 C11 A:COB504 2.8 40.1 1.0 C1 A:COB504 2.8 40.6 1.0 C14 A:COB504 2.9 40.2 1.0 C6 A:COB504 2.9 39.1 1.0 C16 A:COB504 2.9 40.5 1.0 C10 A:COB504 3.1 39.7 1.0 C5 A:COB504 3.2 39.0 1.0 C15 A:COB504 3.3 40.2 1.0 C20 A:COB504 3.7 40.5 1.0 C2 A:COB504 4.0 40.5 1.0 C3 A:COB504 4.1 40.1 1.0 C8 A:COB504 4.1 38.9 1.0 C18 A:COB504 4.1 41.4 1.0 CD1 A:LEU322 4.1 42.1 1.0 C12 A:COB504 4.2 40.2 1.0 C17 A:COB504 4.2 40.7 1.0 C13 A:COB504 4.2 40.2 1.0 C26 A:COB504 4.2 40.9 1.0 C7 A:COB504 4.2 38.8 1.0 O39 A:COB504 4.4 38.2 1.0 CD2 A:LEU322 4.5 42.6 1.0 OH A:TYR23 4.7 48.5 1.0 C35 A:COB504 4.7 38.3 1.0 CG A:LEU322 4.7 41.8 1.0 C54 A:COB504 4.8 40.5 1.0 C53 A:COB504 4.9 39.7 1.0

Cobalt 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 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ B:Co504 b:39.7 occ:1.00 CO B:COB504 0.0 39.7 1.0 N21 B:COB504 1.8 40.0 1.0 N22 B:COB504 1.8 39.6 1.0 N23 B:COB504 1.9 39.7 1.0 N24 B:COB504 1.9 40.1 1.0 C1A B:COB504 2.0 39.8 1.0 C19 B:COB504 2.7 40.3 1.0 C9 B:COB504 2.7 39.5 1.0 C4 B:COB504 2.8 40.0 1.0 C11 B:COB504 2.8 39.7 1.0 C1 B:COB504 2.8 40.4 1.0 C6 B:COB504 2.9 39.7 1.0 C14 B:COB504 2.9 39.6 1.0 C16 B:COB504 2.9 40.0 1.0 C10 B:COB504 3.1 39.5 1.0 C5 B:COB504 3.2 39.6 1.0 C15 B:COB504 3.4 39.4 1.0 C20 B:COB504 3.7 40.6 1.0 C2 B:COB504 3.9 40.7 1.0 C3 B:COB504 4.0 40.4 1.0 C8 B:COB504 4.1 39.5 1.0 C18 B:COB504 4.1 40.4 1.0 CD1 B:LEU322 4.2 45.0 1.0 C26 B:COB504 4.2 41.1 1.0 C12 B:COB504 4.2 39.9 1.0 C13 B:COB504 4.2 39.6 1.0 C7 B:COB504 4.2 39.6 1.0 C17 B:COB504 4.2 40.5 1.0 CD2 B:LEU322 4.4 45.0 1.0 O39 B:COB504 4.4 40.2 1.0 OH B:TYR23 4.6 48.0 1.0 CG B:LEU322 4.7 44.7 1.0 C35 B:COB504 4.7 39.2 1.0 C54 B:COB504 4.8 40.6 1.0 C53 B:COB504 4.9 39.0 1.0

Cobalt 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 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ C:Co504 b:42.3 occ:1.00 CO C:COB504 0.0 42.3 1.0 N21 C:COB504 1.8 42.7 1.0 N22 C:COB504 1.8 42.2 1.0 N23 C:COB504 1.9 42.5 1.0 N24 C:COB504 1.9 42.6 1.0 C1A C:COB504 2.0 42.4 1.0 C19 C:COB504 2.7 42.9 1.0 C9 C:COB504 2.7 42.3 1.0 C4 C:COB504 2.8 42.5 1.0 C11 C:COB504 2.8 42.5 1.0 C1 C:COB504 2.8 43.1 1.0 C14 C:COB504 2.9 42.4 1.0 C6 C:COB504 2.9 42.3 1.0 C16 C:COB504 2.9 42.4 1.0 C10 C:COB504 3.1 42.2 1.0 C5 C:COB504 3.2 41.9 1.0 C15 C:COB504 3.4 41.9 1.0 C20 C:COB504 3.7 43.3 1.0 C2 C:COB504 3.9 43.5 1.0 C3 C:COB504 4.1 43.1 1.0 C8 C:COB504 4.1 42.6 1.0 C18 C:COB504 4.1 42.9 1.0 CD1 C:LEU322 4.1 44.4 1.0 C26 C:COB504 4.2 44.3 1.0 C12 C:COB504 4.2 42.8 1.0 C13 C:COB504 4.2 42.8 1.0 C17 C:COB504 4.2 42.4 1.0 C7 C:COB504 4.2 42.6 1.0 O39 C:COB504 4.4 43.9 1.0 CD2 C:LEU322 4.4 44.7 1.0 OH C:TYR23 4.5 51.4 1.0 CG C:LEU322 4.7 44.2 1.0 C35 C:COB504 4.7 41.1 1.0 C54 C:COB504 4.8 42.3 1.0 C53 C:COB504 4.9 41.1 1.0

Cobalt 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 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-Adenosyl-L-Homocysteine Bound. within 5.0Å range: probe atom residue distance (Å) B Occ D:Co504 b:49.2 occ:1.00 CO D:COB504 0.0 49.2 1.0 N21 D:COB504 1.8 49.0 1.0 N22 D:COB504 1.8 48.9 1.0 N24 D:COB504 1.9 49.0 1.0 N23 D:COB504 1.9 49.0 1.0 C1A D:COB504 2.0 49.3 1.0 C19 D:COB504 2.7 49.0 1.0 C9 D:COB504 2.8 48.6 1.0 C4 D:COB504 2.8 48.9 1.0 C11 D:COB504 2.8 48.9 1.0 C1 D:COB504 2.8 49.0 1.0 C14 D:COB504 2.9 49.0 1.0 C6 D:COB504 2.9 48.7 1.0 C16 D:COB504 2.9 48.7 1.0 C10 D:COB504 3.1 48.5 1.0 C5 D:COB504 3.2 48.5 1.0 C15 D:COB504 3.4 48.6 1.0 C20 D:COB504 3.7 48.9 1.0 C2 D:COB504 3.9 49.2 1.0 C3 D:COB504 4.1 49.2 1.0 C18 D:COB504 4.1 48.8 1.0 C8 D:COB504 4.1 48.6 1.0 C26 D:COB504 4.2 49.6 1.0 C17 D:COB504 4.2 48.6 1.0 C12 D:COB504 4.2 49.0 1.0 C13 D:COB504 4.2 49.1 1.0 C7 D:COB504 4.2 48.6 1.0 CD1 D:LEU322 4.2 58.0 1.0 O39 D:COB504 4.4 49.3 1.0 CD2 D:LEU322 4.5 58.0 1.0 OH D:TYR23 4.7 62.5 1.0 C35 D:COB504 4.7 48.1 1.0 CG D:LEU322 4.8 57.5 1.0 C54 D:COB504 4.8 48.8 1.0 C53 D:COB504 4.9 48.1 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