Chlorine 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:

Iron	(Fe)	8 atoms
Cobalt	(Co)	2 atoms
Potassium	(K)	2 atoms

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

Chlorine 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 Chlorine with other atoms in the Cl 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 B:Cl1919 b:66.2 occ:1.00 ND1 B:HIS264 3.1 30.3 1.0 CE1 B:HIS264 3.9 29.2 1.0 CG B:GLU268 4.1 41.8 1.0 CG B:HIS264 4.2 25.0 1.0 O B:HOH2250 4.3 23.9 1.0 O B:HIS264 4.4 18.2 1.0 OE2 B:GLU268 4.4 58.2 1.0 CB B:HIS264 4.4 18.2 1.0 CB B:ALA267 4.5 15.0 1.0 CA B:HIS264 4.7 20.6 1.0 CG2 B:THR297 4.7 20.6 1.0 CD B:GLU268 4.8 54.3 1.0 C B:HIS264 5.0 19.6 1.0 N B:GLU268 5.0 18.2 1.0

Chlorine 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 Chlorine with other atoms in the Cl 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:Cl1920 b:28.7 occ:1.00 NZ B:LYS225 3.3 49.3 1.0 N B:ARG258 3.3 20.0 1.0 CD B:PRO257 3.4 22.0 1.0 CG B:ARG258 3.6 21.7 1.0 CB B:ARG258 3.6 21.1 1.0 N B:PRO257 3.7 18.4 1.0 CB B:PRO257 3.9 20.1 1.0 CG B:PRO257 4.0 23.3 1.0 CB B:MET256 4.0 23.2 1.0 CE B:LYS225 4.0 45.7 1.0 CA B:ARG258 4.1 18.2 1.0 C B:PRO257 4.2 21.2 1.0 CA B:PRO257 4.2 21.0 1.0 CD B:ARG258 4.2 24.4 1.0 C B:MET256 4.3 18.1 1.0 O B:HOH2199 4.4 40.6 1.0 CA B:MET256 4.6 19.7 1.0 CG B:MET256 4.7 31.5 1.0 SD B:MET256 4.8 37.9 1.0 CD B:LYS225 4.8 42.0 1.0 NE B:ARG258 5.0 21.6 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