Potassium 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
Cobalt	(Co)	2 atoms

The binding sites of Potassium 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 Potassium atom.
In total 4 binding sites of Potassium where determined in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam, PDB code: 7kdy:
Jump to Potassium binding site number: 1; 2; 3; 4;

Potassium binding site 1 out of 4 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 Potassium with other atoms in the K 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:K707 b:18.1 occ:1.00 O A:HOH875 2.5 16.0 1.0 O B:HOH994 2.6 28.5 1.0 O A:HOH876 2.6 15.5 1.0 O A:HOH949 2.6 28.7 1.0 O A:HOH881 2.6 20.8 1.0 O A:HOH909 2.7 13.0 1.0 O B:HOH1044 2.7 25.6 1.0 O B:HOH1410 4.0 41.9 1.0 OD1 A:ASP214 4.2 13.7 1.0 OD2 B:ASP242 4.3 27.3 1.0 O A:SER217 4.4 13.6 1.0 O A:ASN388 4.4 20.4 1.0 O A:HOH1247 4.5 25.5 1.0 O A:HOH1274 4.6 36.1 1.0 OG1 A:THR219 4.6 15.0 1.0 O B:HOH1418 4.6 51.9 1.0 C A:SER217 4.6 11.6 1.0 O A:HOH1012 4.6 17.4 1.0 OD2 A:ASP106 4.8 20.8 1.0 O A:THR219 4.9 12.7 1.0 N A:ALA218 5.0 13.5 1.0

Potassium binding site 2 out of 4 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 Potassium with other atoms in the K 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 A:K708 b:27.7 occ:1.00 O A:HOH1289 3.3 31.5 1.0 N A:ARG258 3.3 17.7 1.0 CD A:PRO257 3.4 17.5 1.0 NZ A:LYS225 3.5 38.4 1.0 CG A:ARG258 3.7 19.4 1.0 N A:PRO257 3.7 14.9 1.0 CB A:ARG258 3.7 16.6 1.0 CB A:PRO257 3.9 14.8 1.0 CG A:PRO257 3.9 19.3 1.0 CB A:MET256 4.0 20.1 1.0 CA A:ARG258 4.2 15.1 1.0 CD A:ARG258 4.2 24.4 1.0 CA A:PRO257 4.2 15.4 1.0 C A:PRO257 4.2 17.4 1.0 CE A:LYS225 4.3 34.4 1.0 C A:MET256 4.3 14.9 1.0 CA A:MET256 4.6 17.6 1.0 O A:HOH846 4.6 34.6 1.0 CG A:MET256 4.7 24.2 1.0 SD A:MET256 4.8 27.2 1.0 CD A:LYS225 4.8 31.1 1.0 O A:HOH802 4.9 42.0 1.0 NE A:ARG258 4.9 23.3 1.0

Potassium binding site 3 out of 4 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 Potassium with other atoms in the K binding site number 3 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:K706 b:23.4 occ:1.00 O B:HOH844 2.5 12.9 1.0 O B:HOH851 2.6 22.9 1.0 O B:HOH1477 2.6 33.5 1.0 O B:HOH938 2.7 36.3 1.0 O B:HOH820 2.7 51.4 1.0 O B:HOH948 2.7 12.1 1.0 O B:HOH1117 2.7 34.6 1.0 O B:HOH943 2.7 29.2 1.0 OD1 B:ASP214 4.2 13.2 1.0 O B:HOH1420 4.4 39.6 1.0 O B:SER217 4.4 11.0 1.0 O B:ASN388 4.5 14.2 1.0 O B:HOH1470 4.6 38.9 1.0 O B:HOH963 4.7 18.0 1.0 C B:SER217 4.7 13.2 1.0 OG1 B:THR219 4.7 12.4 1.0 O B:THR219 4.8 12.1 1.0 OD2 B:ASP106 4.8 22.3 1.0 O B:HOH1333 4.8 27.6 1.0 CE B:MET220 4.9 34.6 1.0 N B:ALA218 4.9 11.5 1.0 N B:THR219 5.0 12.0 1.0

Potassium binding site 4 out of 4 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 Potassium with other atoms in the K binding site number 4 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:K707 b:31.6 occ:1.00 N B:ARG258 3.2 14.4 1.0 CD B:PRO257 3.5 16.3 1.0 CB B:ARG258 3.6 15.3 1.0 CG B:ARG258 3.6 18.3 1.0 N B:PRO257 3.7 17.1 1.0 CB B:MET256 4.0 21.6 1.0 CB B:PRO257 4.0 16.8 1.0 CA B:ARG258 4.0 13.2 1.0 CG B:PRO257 4.1 19.1 1.0 CD B:ARG258 4.1 22.9 1.0 C B:PRO257 4.2 18.2 1.0 CA B:PRO257 4.2 15.0 1.0 C B:MET256 4.3 15.6 1.0 NZ B:LYS225 4.5 51.8 1.0 CA B:MET256 4.6 19.2 1.0 SD B:MET256 4.7 34.8 1.0 CG B:MET256 4.7 29.6 1.0 CD B:LYS225 4.8 34.7 1.0 NE B:ARG258 4.9 28.2 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