Magnesium 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:

Fluorine

(F)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of the Bacterial Ribosomal Decoding Site in Complex with 4'-Deoxy-4'-Fluoro Neomycin Analog, PDB code: 4pdq:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 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 Magnesium with other atoms in the Mg 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 A:Mg101 b:78.8 occ:1.00 O6 A:G13 3.7 68.4 1.0 N7 A:G13 3.8 69.7 1.0 O6 A:G14 3.9 68.7 1.0 C6 A:G13 4.3 68.4 1.0 C5 A:G13 4.4 68.9 1.0 C8 A:G13 4.9 68.6 1.0 N7 A:G14 5.0 72.8 1.0 C6 A:G14 5.0 69.9 1.0

Magnesium binding site 2 out of 2 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 Magnesium with other atoms in the Mg binding site number 2 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:Mg102 b:61.1 occ:1.00 N7 B:G36 3.7 59.2 1.0 O6 B:G36 3.8 66.0 1.0 O6 B:G37 3.9 55.0 1.0 C5 B:G36 4.2 60.3 1.0 C6 B:G36 4.3 63.8 1.0 O6 A:G10 4.6 62.2 1.0 C8 B:G36 4.7 59.5 1.0 N4 B:C38 4.7 55.4 1.0 C6 B:G37 4.9 52.7 1.0 N4 A:C11 5.0 57.5 1.0 N7 B:G37 5.0 57.3 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