Cobalt in PDB 7kdy: Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam, PDB code: 7kdy 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)	44.19 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	84.503, 132.817, 155.509, 90, 90, 90
R / Rfree (%)	15.7 / 18.8

The structure of Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam also contains other interesting chemical elements:

Iron	(Fe)	8 atoms
Potassium	(K)	4 atoms

The binding sites of Cobalt atom in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam (pdb code 7kdy). 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, Methionine, and (2R)- Pantetheinylated Carbapenam, PDB code: 7kdy:
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, Methionine, and (2R)- Pantetheinylated Carbapenam


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range: probe atom residue distance (Å) B Occ A:Co702 b:14.6 occ:1.00 CO A:B12702 0.0 14.6 1.0 N21 A:B12702 1.9 14.2 1.0 N24 A:B12702 1.9 13.4 1.0 N23 A:B12702 1.9 15.9 1.0 N22 A:B12702 1.9 14.3 1.0 O A:HOH1189 2.5 27.3 1.0 C1 A:B12702 2.8 14.6 1.0 C19 A:B12702 2.8 11.0 1.0 C9 A:B12702 2.9 14.3 1.0 C11 A:B12702 2.9 16.8 1.0 C4 A:B12702 2.9 14.2 1.0 C16 A:B12702 3.0 12.6 1.0 C14 A:B12702 3.0 17.9 1.0 C6 A:B12702 3.0 15.8 1.0 C10 A:B12702 3.2 14.1 1.0 C20 A:B12702 3.3 12.3 1.0 C5 A:B12702 3.3 14.2 1.0 C15 A:B12702 3.4 12.0 1.0 CZ3 A:TRP76 3.6 15.8 1.0 CH2 A:TRP76 4.0 14.9 1.0 C2 A:B12702 4.1 11.6 1.0 C18 A:B12702 4.1 9.2 1.0 C3 A:B12702 4.2 13.0 1.0 C8 A:B12702 4.2 16.3 1.0 C12 A:B12702 4.2 20.0 1.0 C17 A:B12702 4.2 9.7 1.0 C13 A:B12702 4.3 15.1 1.0 C7 A:B12702 4.3 18.1 1.0 C26 A:B12702 4.5 13.3 1.0 N40 A:B12702 4.6 24.0 1.0 O A:HOH974 4.6 15.9 1.0 C30 A:B12702 4.8 17.3 1.0 CE3 A:TRP76 4.8 17.2 1.0 C35 A:B12702 4.8 14.1 1.0 C48 A:B12702 4.9 14.2 1.0 C53 A:B12702 4.9 10.2 1.0 C46 A:B12702 4.9 19.9 1.0 C54 A:B12702 4.9 10.3 1.0

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


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, Methionine, and (2R)- Pantetheinylated Carbapenam within 5.0Å range: probe atom residue distance (Å) B Occ B:Co702 b:12.7 occ:1.00 CO B:B12702 0.0 12.7 1.0 N21 B:B12702 1.9 11.5 1.0 N24 B:B12702 1.9 11.6 1.0 N23 B:B12702 1.9 14.9 1.0 N22 B:B12702 1.9 14.2 1.0 O B:HOH1315 2.7 26.2 1.0 C1 B:B12702 2.8 12.0 1.0 C19 B:B12702 2.8 9.5 1.0 C9 B:B12702 2.9 14.2 1.0 C11 B:B12702 2.9 16.9 1.0 C4 B:B12702 2.9 10.9 1.0 C16 B:B12702 3.0 9.7 1.0 C6 B:B12702 3.0 12.8 1.0 C14 B:B12702 3.0 12.7 1.0 C10 B:B12702 3.2 11.8 1.0 C20 B:B12702 3.3 9.0 1.0 C5 B:B12702 3.4 13.2 1.0 C15 B:B12702 3.4 10.0 1.0 CZ3 B:TRP76 3.7 16.7 1.0 CH2 B:TRP76 3.9 19.1 1.0 C2 B:B12702 4.1 11.4 1.0 C18 B:B12702 4.1 6.6 1.0 C3 B:B12702 4.2 11.7 1.0 C8 B:B12702 4.2 17.1 1.0 C12 B:B12702 4.2 17.1 1.0 C17 B:B12702 4.2 8.5 1.0 C13 B:B12702 4.3 13.0 1.0 C7 B:B12702 4.3 13.7 1.0 C26 B:B12702 4.5 11.2 1.0 O B:HOH934 4.5 12.5 1.0 N40 B:B12702 4.6 21.7 1.0 C48 B:B12702 4.8 16.0 1.0 C35 B:B12702 4.8 16.6 1.0 C30 B:B12702 4.8 13.3 1.0 C46 B:B12702 4.9 15.4 1.0 CE3 B:TRP76 4.9 15.0 1.0 C53 B:B12702 4.9 9.3 1.0 C54 B:B12702 5.0 7.8 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