Potassium 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
Cobalt	(Co)	2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, and Methionine, PDB code: 7kdx:
Jump to Potassium binding site number: 1; 2;

Potassium 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 Potassium with other atoms in the K 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:K712 b:21.1 occ:1.00 O A:HOH853 2.5 18.3 1.0 O A:HOH881 2.6 15.2 1.0 O A:HOH886 2.6 26.9 1.0 O B:HOH2063 2.6 28.2 1.0 O A:HOH816 2.6 25.3 1.0 O A:HOH924 2.6 30.7 1.0 O B:HOH2221 2.7 27.4 1.0 OD2 B:ASP242 4.2 34.0 1.0 OD1 A:ASP214 4.2 14.5 1.0 O A:SER217 4.3 17.1 1.0 O A:HOH879 4.5 16.9 1.0 O A:HOH1188 4.5 47.4 1.0 O A:ASN388 4.5 15.7 1.0 C A:SER217 4.6 16.6 1.0 OD2 A:ASP106 4.6 24.9 1.0 O A:THR219 4.6 13.1 1.0 OG1 A:THR219 4.6 14.5 1.0 O A:HOH1149 4.7 30.4 1.0 O B:HOH2254 4.8 43.6 1.0 N A:ALA218 4.9 13.8 1.0 N A:THR219 5.0 13.2 1.0

Potassium 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 Potassium with other atoms in the K 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:K1921 b:22.9 occ:1.00 O B:HOH2058 2.5 17.0 1.0 O B:HOH2131 2.6 15.8 1.0 O B:HOH2244 2.6 28.6 1.0 O B:HOH2049 2.6 26.8 1.0 O B:HOH2020 2.6 28.6 1.0 O B:HOH2097 2.7 36.4 1.0 OD1 B:ASP214 4.2 14.9 1.0 O B:SER217 4.5 14.3 1.0 O B:ASN388 4.5 18.1 1.0 O B:HOH2100 4.5 19.3 1.0 C B:SER217 4.6 13.5 1.0 OG1 B:THR219 4.6 13.7 1.0 O B:THR219 4.7 14.6 1.0 O B:HOH2426 4.7 35.1 1.0 OD2 B:ASP106 4.7 22.5 1.0 N B:ALA218 4.9 14.7 1.0 N B:THR219 4.9 13.7 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