Iron in PDB 6ny6: Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome

The structure of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome, PDB code: 6ny6 was solved by I.J.Pavelich, E.D.Hoffer, T.Maehigashi, C.M.Dunham, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.83 / 3.74
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	401.710, 401.710, 175.440, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 22.4

The structure of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome also contains other interesting chemical elements:

Magnesium	(Mg)	184 atoms
Zinc	(Zn)	1 atom

The binding sites of Iron atom in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome (pdb code 6ny6). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 4 binding sites of Iron where determined in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome, PDB code: 6ny6:
Jump to Iron binding site number: 1; 2; 3; 4;

Iron binding site 1 out of 4 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.5 occ:1.00 FE1 D:SF4301 0.0 0.5 1.0 S2 D:SF4301 2.2 0.7 1.0 S3 D:SF4301 2.3 0.9 1.0 S4 D:SF4301 2.3 1.0 1.0 FE4 D:SF4301 2.7 0.5 1.0 FE3 D:SF4301 2.7 0.4 1.0 FE2 D:SF4301 2.7 0.2 1.0 SG D:CYS9 2.9 0.7 1.0 CA D:CYS9 3.6 0.3 1.0 CB D:CYS9 3.8 0.3 1.0 S1 D:SF4301 3.9 0.9 1.0 N D:CYS9 3.9 0.4 1.0 CG D:LYS22 4.1 0.4 1.0 O D:VAL8 4.1 0.9 1.0 SG D:CYS12 4.1 0.9 1.0 C D:VAL8 4.2 0.6 1.0 CB D:LYS22 4.5 0.1 1.0 CD D:LYS22 4.6 0.4 1.0 NZ D:LYS18 4.7 0.6 1.0 CB D:VAL8 4.9 0.3 1.0 C D:CYS9 4.9 0.8 1.0 CB D:ALA32 4.9 0.6 1.0 CB D:CYS12 5.0 0.5 1.0 CD1 D:LEU21 5.0 0.5 1.0

Iron binding site 2 out of 4 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.2 occ:1.00 FE2 D:SF4301 0.0 0.2 1.0 S1 D:SF4301 2.3 0.9 1.0 S4 D:SF4301 2.3 1.0 1.0 S3 D:SF4301 2.3 0.9 1.0 SG D:CYS12 2.6 0.9 1.0 NZ D:LYS18 2.7 0.6 1.0 FE3 D:SF4301 2.7 0.4 1.0 FE4 D:SF4301 2.7 0.5 1.0 FE1 D:SF4301 2.7 0.5 1.0 CD D:LYS18 3.0 0.5 1.0 CE D:LYS18 3.3 0.7 1.0 CB D:CYS12 3.6 0.5 1.0 S2 D:SF4301 3.9 0.7 1.0 N D:TYR20 4.0 0.2 1.0 CA D:TYR20 4.3 0.4 1.0 SG D:CYS31 4.3 0.5 1.0 N D:LEU21 4.4 0.0 1.0 CG D:LYS18 4.4 0.1 1.0 SG D:CYS26 4.4 0.8 1.0 N D:LEU19 4.6 0.7 1.0 CB D:CYS26 4.8 0.9 1.0 C D:TYR20 4.9 0.1 1.0 CD1 D:LEU21 5.0 0.5 1.0

Iron binding site 3 out of 4 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 3 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.4 occ:1.00 FE3 D:SF4301 0.0 0.4 1.0 S4 D:SF4301 2.2 1.0 1.0 S2 D:SF4301 2.3 0.7 1.0 S1 D:SF4301 2.3 0.9 1.0 FE2 D:SF4301 2.7 0.2 1.0 FE1 D:SF4301 2.7 0.5 1.0 FE4 D:SF4301 2.8 0.5 1.0 N D:ALA32 3.1 0.6 1.0 NZ D:LYS18 3.2 0.6 1.0 SG D:CYS31 3.4 0.5 1.0 CB D:ALA32 3.7 0.6 1.0 SG D:CYS9 3.8 0.7 1.0 CA D:CYS31 3.9 0.7 1.0 S3 D:SF4301 3.9 0.9 1.0 C D:CYS31 4.0 0.1 1.0 CA D:ALA32 4.0 0.6 1.0 CB D:CYS31 4.2 0.6 1.0 CE D:LYS18 4.6 0.7 1.0 CB D:CYS9 4.7 0.3 1.0 N D:MET33 4.8 0.1 1.0 CD D:LYS18 4.8 0.5 1.0 SG D:CYS12 4.9 0.9 1.0 C D:ALA32 5.0 0.9 1.0

Iron binding site 4 out of 4 in the Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 4 of Structure of Dimeric Escherichia Coli Toxin Yoeb Bound to the Thermus Thermophilus 30S Ribosome within 5.0Å range: probe atom residue distance (Å) B Occ D:Fe301 b:0.5 occ:1.00 FE4 D:SF4301 0.0 0.5 1.0 S3 D:SF4301 2.2 0.9 1.0 S1 D:SF4301 2.3 0.9 1.0 S2 D:SF4301 2.3 0.7 1.0 SG D:CYS26 2.6 0.8 1.0 FE1 D:SF4301 2.7 0.5 1.0 FE2 D:SF4301 2.7 0.2 1.0 FE3 D:SF4301 2.8 0.4 1.0 CB D:LYS22 3.3 0.1 1.0 CB D:CYS26 3.6 0.9 1.0 CA D:CYS26 3.8 0.1 1.0 CG D:LYS22 3.8 0.4 1.0 S4 D:SF4301 3.9 1.0 1.0 N D:CYS26 4.0 0.7 1.0 N D:LYS22 4.0 0.1 1.0 N D:LEU21 4.3 0.0 1.0 CA D:LYS22 4.3 0.3 1.0 C D:ARG25 4.5 0.5 1.0 CA D:TYR20 4.6 0.4 1.0 C D:LEU21 4.6 0.2 1.0 CD D:LYS22 4.6 0.4 1.0 C D:TYR20 4.8 0.1 1.0 NZ D:LYS18 4.8 0.6 1.0 O D:ARG25 4.9 0.8 1.0 N D:GLY23 4.9 0.9 1.0 CB D:ARG25 4.9 0.2 1.0 C D:LYS22 4.9 0.3 1.0 SG D:CYS9 5.0 0.7 1.0

I.J.Pavelich, T.Maehigashi, E.D.Hoffer, A.Ruangprasert, S.J.Miles, C.M.Dunham. Monomeric Yoeb Toxin Retains Rnase Activity But Adopts An Obligate Dimeric Form For Thermal Stability. Nucleic Acids Res. V. 47 10400 2019.
ISSN: ESSN 1362-4962
PubMed: 31501867
DOI: 10.1093/NAR/GKZ760