Iron 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:

Potassium	(K)	4 atoms
Cobalt	(Co)	2 atoms

The binding sites of Iron 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 Iron atom.
In total 8 binding sites of Iron where determined in the Crystal Structure of Streptomyces Tokunonesis Tokk with Hydroxycobalamin, 5'-Deoxyadenosine, Methionine, and (2R)- Pantetheinylated Carbapenam, PDB code: 7kdy:
Jump to Iron binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Iron binding site 1 out of 8 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 Iron with other atoms in the Fe 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:Fe701 b:14.5 occ:1.00 FE1 A:SF4701 0.0 14.5 1.0 S4 A:SF4701 2.2 13.8 1.0 S3 A:SF4701 2.2 15.7 1.0 S2 A:SF4701 2.3 13.3 1.0 SG A:CYS210 2.5 17.3 1.0 FE2 A:SF4701 2.7 13.4 1.0 FE4 A:SF4701 2.7 14.6 1.0 FE3 A:SF4701 2.7 14.5 1.0 CB A:CYS210 3.2 15.5 1.0 NH1 A:ARG324 3.6 12.6 1.0 S1 A:SF4701 3.8 13.2 1.0 O A:MET703 3.9 13.3 1.0 N A:CYS210 4.1 16.2 1.0 CA A:CYS210 4.3 16.3 1.0 CB A:TYR208 4.6 17.3 1.0 CB A:CYS213 4.7 14.9 1.0 O A:HOH897 4.7 17.3 1.0 SG A:CYS206 4.8 14.0 1.0 N A:MET703 4.8 14.2 1.0 SG A:CYS213 4.9 14.7 1.0 CZ A:PHE212 4.9 16.8 1.0 CZ A:ARG324 4.9 16.6 1.0 CD A:LYS285 4.9 18.5 1.0 C A:MET703 5.0 16.2 1.0

Iron binding site 2 out of 8 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 Iron with other atoms in the Fe 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:Fe701 b:13.4 occ:1.00 FE2 A:SF4701 0.0 13.4 1.0 S3 A:SF4701 2.2 15.7 1.0 S1 A:SF4701 2.3 13.2 1.0 S4 A:SF4701 2.3 13.8 1.0 SG A:CYS206 2.4 14.0 1.0 FE1 A:SF4701 2.7 14.5 1.0 FE4 A:SF4701 2.7 14.6 1.0 FE3 A:SF4701 2.8 14.5 1.0 CB A:CYS206 3.4 13.9 1.0 S2 A:SF4701 3.8 13.3 1.0 N A:MET703 4.1 14.2 1.0 CB A:TYR208 4.2 17.3 1.0 CD2 A:TYR208 4.4 12.8 1.0 ND2 A:ASN252 4.5 10.1 1.0 CA A:CYS206 4.8 11.0 1.0 O A:MET703 4.8 13.3 1.0 CG A:TYR208 4.8 15.1 1.0 CB A:ALA251 4.8 11.9 1.0 N A:TYR208 4.9 18.3 1.0 CA A:TYR208 4.9 19.8 1.0 C A:TYR208 4.9 16.3 1.0 SG A:CYS213 4.9 14.7 1.0 CG2 A:THR219 4.9 13.7 1.0 SG A:CYS210 4.9 17.3 1.0

Iron binding site 3 out of 8 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 Iron with other atoms in the Fe 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 A:Fe701 b:14.5 occ:1.00 FE3 A:SF4701 0.0 14.5 1.0 S2 A:SF4701 2.3 13.3 1.0 S1 A:SF4701 2.3 13.2 1.0 S4 A:SF4701 2.3 13.8 1.0 O A:MET703 2.4 13.3 1.0 N A:MET703 2.4 14.2 1.0 FE1 A:SF4701 2.7 14.5 1.0 SD A:MET703 2.8 13.2 1.0 FE4 A:SF4701 2.8 14.6 1.0 FE2 A:SF4701 2.8 13.4 1.0 C A:MET703 3.2 16.2 1.0 CA A:MET703 3.3 13.4 1.0 CE A:MET703 3.7 11.6 1.0 CG A:MET703 3.7 9.0 1.0 S3 A:SF4701 3.9 15.7 1.0 CB A:MET703 3.9 12.2 1.0 NH1 A:ARG324 4.2 12.6 1.0 OXT A:MET703 4.3 15.4 1.0 O A:ALA251 4.8 11.3 1.0 SG A:CYS206 4.8 14.0 1.0 OD1 A:ASN252 5.0 13.3 1.0

Iron binding site 4 out of 8 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 Iron with other atoms in the Fe 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 A:Fe701 b:14.6 occ:1.00 FE4 A:SF4701 0.0 14.6 1.0 S1 A:SF4701 2.2 13.2 1.0 S3 A:SF4701 2.3 15.7 1.0 S2 A:SF4701 2.3 13.3 1.0 SG A:CYS213 2.5 14.7 1.0 FE2 A:SF4701 2.7 13.4 1.0 FE1 A:SF4701 2.7 14.5 1.0 FE3 A:SF4701 2.8 14.5 1.0 CB A:CYS213 3.2 14.9 1.0 S4 A:SF4701 3.8 13.8 1.0 SD A:MET703 4.2 13.2 1.0 CB A:TRP215 4.3 10.6 1.0 CG2 A:THR219 4.6 13.7 1.0 CB A:CYS210 4.6 15.5 1.0 CA A:CYS213 4.7 15.8 1.0 CE A:MET703 4.8 11.6 1.0 SG A:CYS210 4.9 17.3 1.0 CE3 A:TRP215 4.9 13.9 1.0 CG A:TRP215 4.9 12.4 1.0 O A:MET703 4.9 13.3 1.0 SG A:CYS206 4.9 14.0 1.0 CE1 A:PHE212 4.9 14.8 1.0 N A:MET703 5.0 14.2 1.0

Iron binding site 5 out of 8 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 Iron with other atoms in the Fe binding site number 5 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:Fe701 b:12.3 occ:1.00 FE1 B:SF4701 0.0 12.3 1.0 S3 B:SF4701 2.2 10.6 1.0 S2 B:SF4701 2.3 12.2 1.0 S4 B:SF4701 2.3 10.4 1.0 SG B:CYS210 2.5 12.3 1.0 FE4 B:SF4701 2.7 11.4 1.0 FE3 B:SF4701 2.7 11.7 1.0 FE2 B:SF4701 2.8 11.2 1.0 CB B:CYS210 3.2 11.1 1.0 NH1 B:ARG324 3.6 9.3 1.0 S1 B:SF4701 3.9 10.1 1.0 OXT B:MET703 3.9 12.1 1.0 N B:CYS210 4.1 13.0 1.0 CA B:CYS210 4.3 11.7 1.0 CB B:TYR208 4.6 11.7 1.0 CB B:CYS213 4.6 9.7 1.0 O B:HOH932 4.7 11.6 1.0 SG B:CYS213 4.8 12.4 1.0 SG B:CYS206 4.9 11.0 1.0 CZ B:ARG324 4.9 10.2 1.0 N B:MET703 4.9 10.8 1.0 CZ B:PHE212 4.9 14.1 1.0 CD B:LYS285 4.9 14.0 1.0

Iron binding site 6 out of 8 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 Iron with other atoms in the Fe binding site number 6 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:Fe701 b:11.2 occ:1.00 FE2 B:SF4701 0.0 11.2 1.0 S4 B:SF4701 2.3 10.4 1.0 S1 B:SF4701 2.3 10.1 1.0 S3 B:SF4701 2.4 10.6 1.0 OXT B:MET703 2.4 12.1 1.0 N B:MET703 2.5 10.8 1.0 SD B:MET703 2.8 11.7 1.0 FE3 B:SF4701 2.8 11.7 1.0 FE1 B:SF4701 2.8 12.3 1.0 FE4 B:SF4701 2.8 11.4 1.0 C B:MET703 3.2 13.6 1.0 CA B:MET703 3.3 9.3 1.0 CE B:MET703 3.7 9.1 1.0 CG B:MET703 3.7 8.4 1.0 CB B:MET703 3.9 8.6 1.0 S2 B:SF4701 3.9 12.2 1.0 NH1 B:ARG324 4.2 9.3 1.0 O B:MET703 4.4 13.6 1.0 O B:ALA251 4.7 10.1 1.0 SG B:CYS206 4.9 11.0 1.0 OD1 B:ASN252 4.9 9.8 1.0

Iron binding site 7 out of 8 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 Iron with other atoms in the Fe binding site number 7 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:Fe701 b:11.7 occ:1.00 FE3 B:SF4701 0.0 11.7 1.0 S1 B:SF4701 2.2 10.1 1.0 S2 B:SF4701 2.3 12.2 1.0 S4 B:SF4701 2.3 10.4 1.0 SG B:CYS213 2.5 12.4 1.0 FE4 B:SF4701 2.7 11.4 1.0 FE1 B:SF4701 2.7 12.3 1.0 FE2 B:SF4701 2.8 11.2 1.0 CB B:CYS213 3.2 9.7 1.0 S3 B:SF4701 3.8 10.6 1.0 SD B:MET703 4.2 11.7 1.0 CB B:TRP215 4.3 8.0 1.0 CG2 B:THR219 4.6 10.9 1.0 CA B:CYS213 4.7 10.8 1.0 CB B:CYS210 4.7 11.1 1.0 CE3 B:TRP215 4.8 11.9 1.0 SG B:CYS210 4.8 12.3 1.0 CE B:MET703 4.8 9.1 1.0 CG B:TRP215 4.9 8.1 1.0 SG B:CYS206 4.9 11.0 1.0 OXT B:MET703 4.9 12.1 1.0 CE1 B:PHE212 4.9 16.1 1.0

Iron binding site 8 out of 8 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 Iron with other atoms in the Fe binding site number 8 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:Fe701 b:11.4 occ:1.00 FE4 B:SF4701 0.0 11.4 1.0 S2 B:SF4701 2.2 12.2 1.0 S3 B:SF4701 2.3 10.6 1.0 S1 B:SF4701 2.3 10.1 1.0 SG B:CYS206 2.4 11.0 1.0 FE1 B:SF4701 2.7 12.3 1.0 FE3 B:SF4701 2.7 11.7 1.0 FE2 B:SF4701 2.8 11.2 1.0 CB B:CYS206 3.4 11.5 1.0 S4 B:SF4701 3.9 10.4 1.0 N B:MET703 4.2 10.8 1.0 CB B:TYR208 4.2 11.7 1.0 CD2 B:TYR208 4.4 11.7 1.0 ND2 B:ASN252 4.5 7.7 1.0 CG2 B:THR219 4.8 10.9 1.0 CB B:ALA251 4.8 7.4 1.0 CA B:CYS206 4.8 9.7 1.0 CG B:TYR208 4.8 11.9 1.0 N B:TYR208 4.9 9.8 1.0 OXT B:MET703 4.9 12.1 1.0 CA B:TYR208 4.9 12.3 1.0 SG B:CYS213 4.9 12.4 1.0 C B:TYR208 4.9 13.7 1.0 SG B:CYS210 4.9 12.3 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