Fluorine in PDB 3wru: Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group

The structure of Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group, PDB code: 3wru was solved by J.P.Maianti, H.Kanazawa, P.Dozzo, L.A.Feeney, E.S.Armstrong, J.Kondo, S.Hanessian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 2.30
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.554, 32.602, 51.413, 90.00, 108.50, 90.00
R / Rfree (%)	24.9 / 26.2

The structure of Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Fluorine atom in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group (pdb code 3wru). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group, PDB code: 3wru:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group


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 Synthetic Aminoglycoside with F-Haba Group within 5.0Å range: probe atom residue distance (Å) B Occ A:F101 b:54.9 occ:1.00 F99 A:SJP101 0.0 54.9 1.0 C24 A:SJP101 1.4 55.6 1.0 C27 A:SJP101 2.3 55.9 1.0 C28 A:SJP101 2.3 55.6 1.0 O19 A:SJP101 2.7 55.5 1.0 C26 A:SJP101 2.9 55.0 1.0 N3 A:SJP101 3.2 54.2 1.0 N4 A:C21 3.2 59.2 1.0 N7 A:SJP101 3.2 52.8 1.0 O6 A:G22 3.4 51.0 1.0 O6 B:G28 3.5 56.9 1.0 N4 B:C27 3.6 61.2 1.0 O2 A:SJP101 3.6 56.8 1.0 O B:HOH227 3.9 34.6 1.0 O B:HOH203 4.2 37.0 1.0 O12 A:SJP101 4.4 49.8 1.0 C7 A:SJP101 4.4 51.4 1.0 C6 A:G22 4.5 52.3 1.0 C4 A:C21 4.5 59.8 1.0 O4 A:U20 4.5 52.4 1.0 C6 B:G28 4.7 58.0 1.0 C4 B:C27 4.8 63.0 1.0 C12 A:SJP101 4.9 50.8 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with Synthetic Aminoglycoside with F-Haba Group within 5.0Å range: probe atom residue distance (Å) B Occ B:F101 b:38.4 occ:1.00 F99 B:SJP101 0.0 38.4 1.0 C24 B:SJP101 1.4 39.2 1.0 C27 B:SJP101 2.3 40.4 1.0 C28 B:SJP101 2.3 38.0 1.0 O19 B:SJP101 2.7 36.7 1.0 N4 B:C44 2.9 29.8 1.0 C26 B:SJP101 3.0 35.8 1.0 N3 B:SJP101 3.0 41.7 1.0 N4 A:C4 3.1 50.3 1.0 O6 B:G45 3.1 40.8 1.0 O6 A:G5 3.2 36.8 1.0 N7 B:SJP101 3.5 32.2 1.0 O2 B:SJP101 3.7 36.7 1.0 O A:HOH202 3.9 28.2 1.0 C4 B:C44 4.1 30.1 1.0 C6 B:G45 4.2 39.0 1.0 O4 B:U43 4.3 32.3 1.0 C4 A:C4 4.4 51.1 1.0 C6 A:G5 4.4 35.7 1.0 O12 B:SJP101 4.6 27.2 1.0 C7 B:SJP101 4.7 31.4 1.0 O A:HOH208 4.8 33.1 1.0 C5 B:C44 4.9 29.3 1.0 N1 B:G45 4.9 37.9 1.0

J.P.Maianti, H.Kanazawa, P.Dozzo, R.D.Matias, L.A.Feeney, E.S.Armstrong, D.J.Hildebrandt, T.R.Kane, M.J.Gliedt, A.A.Goldblum, M.S.Linsell, J.B.Aggen, J.Kondo, S.Hanessian. Toxicity Modulation, Resistance Enzyme Evasion, and A-Site X-Ray Structure of Broad-Spectrum Antibacterial Neomycin Analogs Acs Chem.Biol. V. 9 2067 2014.
ISSN: ISSN 1554-8929
PubMed: 25019242
DOI: 10.1021/CB5003416