Zinc in PDB 2f4v: 30S Ribosome + Designer Antibiotic

The structure of 30S Ribosome + Designer Antibiotic, PDB code: 2f4v was solved by J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 3.80
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	403.323, 403.323, 176.685, 90.00, 90.00, 90.00
R / Rfree (%)	25.9 / 31.5

The structure of 30S Ribosome + Designer Antibiotic also contains other interesting chemical elements:

Magnesium	(Mg)	101 atoms
Potassium	(K)	12 atoms
Chlorine	(Cl)	1 atom

The binding sites of Zinc atom in the 30S Ribosome + Designer Antibiotic (pdb code 2f4v). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the 30S Ribosome + Designer Antibiotic, PDB code: 2f4v:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn306 b:88.4 occ:1.00 SG D:CYS31 1.1 0.6 1.0 SG D:CYS26 1.2 0.7 1.0 SG D:CYS12 1.6 0.0 1.0 SG D:CYS9 2.2 0.3 1.0 CB D:CYS31 2.6 0.1 1.0 CB D:CYS26 2.7 0.8 1.0 CB D:CYS12 3.0 0.9 1.0 CB D:CYS9 3.4 0.2 1.0 CA D:CYS26 3.4 0.2 1.0 O D:LEU19 3.4 0.6 1.0 CA D:CYS9 3.5 0.6 1.0 CD1 D:LEU21 3.6 0.2 1.0 CA D:CYS31 3.8 0.8 1.0 O D:CYS31 4.1 0.0 1.0 O D:CYS26 4.3 0.3 1.0 C D:CYS26 4.3 0.1 1.0 CA D:CYS12 4.4 0.1 1.0 C D:CYS31 4.4 0.1 1.0 C D:CYS9 4.4 0.6 1.0 O D:CYS9 4.6 0.8 1.0 N D:CYS9 4.6 0.5 1.0 N D:CYS26 4.6 0.9 1.0 C D:LEU19 4.7 1.0 1.0 CG D:LEU21 4.8 0.3 1.0 N D:CYS31 5.0 0.9 1.0

Zinc binding site 2 out of 2 in the 30S Ribosome + Designer Antibiotic


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of 30S Ribosome + Designer Antibiotic within 5.0Å range: probe atom residue distance (Å) B Occ N:Zn307 b:0.3 occ:1.00 SG N:CYS43 1.2 72.0 1.0 SG N:CYS40 2.3 72.2 1.0 CB N:CYS27 2.7 75.3 1.0 CB N:CYS43 2.8 70.4 1.0 SG N:CYS27 3.0 69.4 1.0 CA N:CYS43 3.3 71.0 1.0 N N:CYS43 3.4 71.8 1.0 N N:CYS27 3.5 82.9 1.0 CA N:CYS27 3.6 80.5 1.0 N2 A:G1202 3.8 73.1 1.0 SG N:CYS24 3.9 89.9 1.0 CB N:CYS40 4.0 72.0 1.0 N N:CYS40 4.2 74.7 1.0 CD N:ARG26 4.3 90.5 1.0 CB N:ARG26 4.3 87.7 1.0 NH1 N:ARG26 4.4 93.4 1.0 O N:CYS40 4.4 71.6 1.0 CA N:CYS40 4.5 72.8 1.0 N3 A:G1202 4.5 71.8 1.0 C N:ARG26 4.6 84.6 1.0 C2 A:G1202 4.6 72.1 1.0 C N:CYS40 4.7 72.2 1.0 C N:CYS43 4.7 71.5 1.0 C N:ILE42 4.7 72.2 1.0 CB N:ILE42 4.8 70.0 1.0 C N:CYS27 4.9 82.5 1.0 CG N:ARG26 4.9 89.1 1.0 CA N:ARG26 5.0 87.0 1.0

J.B.Murray, S.O.Meroueh, R.J.Russell, G.Lentzen, J.Haddad, S.Mobashery. Interactions of Designer Antibiotics and the Bacterial Ribosome Aminoacyl-Trna Site Chem.Biol. V. 13 129 2006.
ISSN: ISSN 1074-5521
PubMed: 16492561
DOI: 10.1016/J.CHEMBIOL.2005.11.004