Fluorine in PDB 4pdq: Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog

The structure of Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog, PDB code: 4pdq was solved by S.Hanessian, O.M.Saavedra, M.A.Vilchis-Reyes, J.P.Maianti, H.Kanazawa, P.Dozzo, L.A.Feeney, E.S.Armstrong, J.Kondo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.60 / 3.00
Space group	H 3
Cell size a, b, c (Å), α, β, γ (°)	103.657, 103.657, 44.572, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 23.6

The structure of Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog (pdb code 4pdq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total only one binding site of Fluorine was determined in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog, PDB code: 4pdq:

Fluorine binding site 1 out of 1 in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog within 5.0Å range: probe atom residue distance (Å) B Occ B:F101 b:62.7 occ:1.00 F99 B:NMZ101 0.0 62.7 1.0 C4 B:NMZ101 1.4 59.7 1.0 C3 B:NMZ101 2.4 60.0 1.0 C5 B:NMZ101 2.4 60.4 1.0 N3 B:G39 2.6 60.2 1.0 O23 B:NMZ101 2.7 59.1 1.0 C2 B:G39 2.7 59.5 1.0 C4 B:G39 2.8 62.9 1.0 C6 B:NMZ101 2.9 59.9 1.0 O5 B:NMZ101 2.9 61.8 1.0 C2 B:NMZ101 2.9 60.7 1.0 N1 B:G39 3.1 60.1 1.0 C5 B:G39 3.2 62.3 1.0 N2 B:G39 3.4 60.8 1.0 C6 B:G39 3.4 61.2 1.0 C1 B:NMZ101 3.5 59.4 1.0 N9 B:G39 3.5 64.3 1.0 C2' B:G39 3.7 69.6 1.0 N7 B:G39 4.1 63.2 1.0 C1' B:G39 4.1 67.8 1.0 C8 B:G39 4.2 64.2 1.0 N6 B:NMZ101 4.2 60.1 1.0 N2 B:NMZ101 4.3 59.7 1.0 O6 B:G39 4.4 60.0 1.0 O2' B:G39 4.4 72.1 1.0 O1 B:NMZ101 4.5 60.8 1.0 C3' B:G39 4.6 69.6 1.0 OP2 B:A41 4.8 70.1 1.0

S.Hanessian, O.M.Saavedra, M.A.Vilchis-Reyes, J.P.Maianti, H.Kanazawa, P.Dozzo, R.D.Matias, A.Serio, J.Kondo. Synthesis, Broad Spectrum Antibacterial Activity, and X-Ray Co-Crystal Structure of the Decoding Bacterial Ribosomal A-Site with 4'-Deoxy-4'-Fluoro Neomycin Analogs Chem Sci V. 5 4621 2014.
ISSN: ESSN 2041-6539
DOI: 10.1039/C4SC01626B