Fluorine in PDB 5qaf: Oxa-48 in Complex with Compound 8C

All present enzymatic activity of Oxa-48 in Complex with Compound 8C:
3.5.2.6;

The structure of Oxa-48 in Complex with Compound 8C, PDB code: 5qaf was solved by B.A.Lund, H.K.S.Leiros, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.80 / 2.15
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	88.407, 107.087, 124.881, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 22.5

The structure of Oxa-48 in Complex with Compound 8C also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Oxa-48 in Complex with Compound 8C (pdb code 5qaf). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Oxa-48 in Complex with Compound 8C, PDB code: 5qaf:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Oxa-48 in Complex with Compound 8C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Oxa-48 in Complex with Compound 8C within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:68.4 occ:0.87 F A:S1D301 0.0 68.4 0.9 C10 A:S1D301 1.4 66.1 0.9 C9 A:S1D301 2.3 66.3 0.9 C11 A:S1D301 2.3 62.0 0.9 H5 A:S1D301 2.6 79.6 0.9 H6 A:S1D301 2.6 74.5 0.9 HE2 A:TYR211 3.3 48.3 1.0 C8 A:S1D301 3.6 65.6 0.9 C12 A:S1D301 3.6 60.6 0.9 C7 A:S1D301 4.1 63.2 0.9 CE2 A:TYR211 4.2 40.2 1.0 HD11 A:ILE102 4.3 69.7 1.0 HB3 A:SER244 4.3 79.1 1.0 H4 A:S1D301 4.5 78.8 0.9 H7 A:S1D301 4.5 72.8 0.9 HD2 A:TYR211 4.5 47.4 1.0 HG21 A:THR213 4.7 52.5 1.0 CD2 A:TYR211 4.8 39.5 1.0 O A:HOH541 4.9 55.7 1.0

Fluorine binding site 2 out of 4 in the Oxa-48 in Complex with Compound 8C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Oxa-48 in Complex with Compound 8C within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:74.9 occ:0.87 F B:S1D301 0.0 74.9 0.9 C10 B:S1D301 1.4 74.3 0.9 C9 B:S1D301 2.3 72.0 0.9 C11 B:S1D301 2.3 70.9 0.9 H5 B:S1D301 2.6 86.4 0.9 H6 B:S1D301 2.6 85.1 0.9 O B:HOH494 3.2 46.2 1.0 HE2 B:TYR211 3.3 57.4 1.0 C8 B:S1D301 3.6 70.0 0.9 C12 B:S1D301 3.6 67.2 0.9 C7 B:S1D301 4.1 69.0 0.9 HB3 B:SER244 4.2 72.1 1.0 CE2 B:TYR211 4.2 47.8 1.0 HD2 B:TYR211 4.4 55.8 1.0 H4 B:S1D301 4.5 84.1 0.9 H7 B:S1D301 4.5 80.6 0.9 HD11 B:ILE102 4.5 68.8 1.0 HH B:TYR211 4.6 64.4 1.0 HB2 B:SER244 4.8 72.1 1.0 CD2 B:TYR211 4.8 46.4 1.0 O B:HOH550 4.9 53.1 1.0 CB B:SER244 4.9 60.1 1.0 HG12 B:ILE102 5.0 66.8 1.0

Fluorine binding site 3 out of 4 in the Oxa-48 in Complex with Compound 8C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Oxa-48 in Complex with Compound 8C within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:72.1 occ:0.87 F C:S1D301 0.0 72.1 0.9 C10 C:S1D301 1.4 65.5 0.9 C9 C:S1D301 2.3 58.2 0.9 C11 C:S1D301 2.3 63.8 0.9 H5 C:S1D301 2.6 69.9 0.9 H6 C:S1D301 2.6 76.6 0.9 HE2 C:TYR211 3.6 52.9 1.0 C8 C:S1D301 3.6 52.1 0.9 C12 C:S1D301 3.6 58.0 0.9 HB3 C:SER244 3.9 47.1 1.0 C7 C:S1D301 4.1 53.2 0.9 H4 C:S1D301 4.5 62.6 0.9 H7 C:S1D301 4.5 69.6 0.9 CE2 C:TYR211 4.5 44.0 1.0 CB C:SER244 4.6 39.2 1.0 HD13 C:ILE102 4.6 50.6 1.0 HB2 C:SER244 4.6 47.1 1.0 OG C:SER244 4.7 42.9 1.0

Fluorine binding site 4 out of 4 in the Oxa-48 in Complex with Compound 8C


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Oxa-48 in Complex with Compound 8C within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:72.6 occ:0.87 F D:S1D301 0.0 72.6 0.9 C10 D:S1D301 1.4 63.4 0.9 C9 D:S1D301 2.3 61.5 0.9 C11 D:S1D301 2.3 56.4 0.9 H5 D:S1D301 2.6 73.9 0.9 H6 D:S1D301 2.6 67.8 0.9 O D:HOH552 3.4 56.3 1.0 HE2 D:TYR211 3.6 48.2 1.0 C8 D:S1D301 3.6 58.7 0.9 C12 D:S1D301 3.6 53.1 0.9 C7 D:S1D301 4.1 57.1 0.9 HB3 D:SER244 4.3 43.4 1.0 CE2 D:TYR211 4.4 40.2 1.0 O D:HOH565 4.5 51.7 1.0 H4 D:S1D301 4.5 70.5 0.9 H7 D:S1D301 4.5 63.8 0.9 HH D:TYR211 4.5 50.9 1.0 HG D:SER244 4.7 51.5 1.0 HD11 D:ILE102 4.7 52.3 1.0 HD2 D:TYR211 4.9 47.0 1.0

S.Akhter, B.A.Lund, A.Ismael, M.Langer, J.Isaksson, T.Christopeit, H.S.Leiros, A.Bayer. A Focused Fragment Library Targeting the Antibiotic Resistance Enzyme - Oxacillinase-48: Synthesis, Structural Evaluation and Inhibitor Design. Eur J Med Chem V. 145 634 2018.
ISSN: ISSN 1768-3254
PubMed: 29348071
DOI: 10.1016/J.EJMECH.2017.12.085