Cobalt in PDB 7kdx: Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx was solved by H.L.Knox, S.J.Booker, A.K.Boal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.35 / 1.79
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.644, 137.739, 77.914, 90, 90.47, 90
R / Rfree (%)	16.5 / 19.3

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine also contains other interesting chemical elements:

Chlorine	(Cl)	2 atoms
Iron	(Fe)	8 atoms
Potassium	(K)	2 atoms

The binding sites of Cobalt atom in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine (pdb code 7kdx). This binding sites where shown within 5.0 Angstroms radius around Cobalt atom.
In total 2 binding sites of Cobalt where determined in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx:
Jump to Cobalt binding site number: 1; 2;

Cobalt binding site 1 out of 2 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 1 of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ A:Co703 b:13.9 occ:1.00 CO A:B12703 0.0 13.9 1.0 N21 A:B12703 1.9 13.0 1.0 N24 A:B12703 1.9 12.7 1.0 N23 A:B12703 1.9 13.8 1.0 N22 A:B12703 1.9 12.5 1.0 O A:HOH1109 2.6 35.4 1.0 C19 A:B12703 2.8 11.1 1.0 C1 A:B12703 2.8 10.6 1.0 C9 A:B12703 2.9 15.4 1.0 C11 A:B12703 2.9 15.4 1.0 C4 A:B12703 2.9 13.2 1.0 C16 A:B12703 3.0 12.2 1.0 C14 A:B12703 3.0 14.6 1.0 C6 A:B12703 3.0 14.9 1.0 C10 A:B12703 3.2 20.3 1.0 C5 A:B12703 3.4 16.4 1.0 C15 A:B12703 3.4 13.5 1.0 C20 A:B12703 3.4 8.6 1.0 CZ3 A:TRP76 3.8 13.7 1.0 CH2 A:TRP76 4.1 15.1 1.0 C18 A:B12703 4.1 12.6 1.0 C2 A:B12703 4.1 9.8 1.0 C3 A:B12703 4.2 11.6 1.0 C17 A:B12703 4.2 10.6 1.0 C12 A:B12703 4.2 16.4 1.0 C8 A:B12703 4.2 15.5 1.0 C13 A:B12703 4.2 16.1 1.0 C7 A:B12703 4.3 17.0 1.0 N40 A:B12703 4.5 20.1 1.0 C26 A:B12703 4.5 8.4 1.0 O A:HOH856 4.7 14.8 1.0 C48 A:B12703 4.8 18.2 1.0 C35 A:B12703 4.8 15.3 1.0 C53 A:B12703 4.9 14.4 1.0 C30 A:B12703 4.9 15.5 1.0 C46 A:B12703 4.9 19.3 1.0 C54 A:B12703 4.9 11.8 1.0 CE3 A:TRP76 5.0 16.3 1.0

Cobalt binding site 2 out of 2 in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine


Mono view


Stereo pair view

A full contact list of Cobalt with other atoms in the Co binding site number 2 of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine within 5.0Å range: probe atom residue distance (Å) B Occ B:Co1902 b:12.8 occ:1.00 CO B:B121902 0.0 12.8 1.0 N21 B:B121902 1.9 12.1 1.0 N24 B:B121902 1.9 8.5 1.0 N23 B:B121902 1.9 12.8 1.0 N22 B:B121902 1.9 14.2 1.0 O B:HOH2363 2.5 29.8 1.0 C19 B:B121902 2.8 11.7 1.0 C1 B:B121902 2.8 10.3 1.0 C9 B:B121902 2.9 16.2 1.0 C11 B:B121902 2.9 14.0 1.0 C4 B:B121902 2.9 9.6 1.0 C16 B:B121902 3.0 10.6 1.0 C14 B:B121902 3.0 12.6 1.0 C6 B:B121902 3.0 12.7 1.0 C10 B:B121902 3.2 15.0 1.0 C5 B:B121902 3.4 14.0 1.0 C15 B:B121902 3.4 11.7 1.0 C20 B:B121902 3.4 9.5 1.0 CZ3 B:TRP76 3.8 13.1 1.0 CH2 B:TRP76 4.0 13.8 1.0 C18 B:B121902 4.1 10.8 1.0 C2 B:B121902 4.1 8.4 1.0 C3 B:B121902 4.2 9.8 1.0 C12 B:B121902 4.2 15.8 1.0 C8 B:B121902 4.2 19.5 1.0 C17 B:B121902 4.2 12.0 1.0 C13 B:B121902 4.2 13.7 1.0 C7 B:B121902 4.3 16.5 1.0 C26 B:B121902 4.5 10.8 1.0 N40 B:B121902 4.5 18.6 1.0 O B:HOH2032 4.7 16.1 1.0 C48 B:B121902 4.8 17.6 1.0 C46 B:B121902 4.8 18.1 1.0 C35 B:B121902 4.8 15.2 1.0 C53 B:B121902 4.9 13.5 1.0 C30 B:B121902 4.9 12.3 1.0 C54 B:B121902 4.9 11.3 1.0 CE3 B:TRP76 5.0 14.2 1.0

H.L.Knox, E.K.Sinner, C.A.Townsend, A.K.Boal, S.J.Booker. Structure of A B 12 -Dependent Radical Sam Enzyme in Carbapenem Biosynthesis. Nature V. 602 343 2022.
ISSN: ESSN 1476-4687
PubMed: 35110734
DOI: 10.1038/S41586-021-04392-4