Fluorine in PDB 5qae: Oxa-48 in Complex with Compound 8B

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

The structure of Oxa-48 in Complex with Compound 8B, PDB code: 5qae 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)	46.81 / 2.10
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	90.302, 109.463, 125.187, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 24

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

Chlorine

(Cl)

2 atoms

The binding sites of Fluorine atom in the Oxa-48 in Complex with Compound 8B (pdb code 5qae). 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 8B, PDB code: 5qae:
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 8B


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:48.3 occ:0.50 F A:Q4G301 0.0 48.3 0.5 C8 A:Q4G301 1.4 29.6 0.5 C7 A:Q4G301 2.3 24.1 0.5 C9 A:Q4G301 2.3 19.3 0.5 H4 A:Q4G301 2.6 23.2 0.5 H3 A:Q4G301 2.6 29.0 0.5 C6 A:Q4G301 3.6 21.5 0.5 C4 A:Q4G301 3.6 22.4 0.5 HE2 A:TYR211 3.7 34.2 1.0 O A:HOH535 4.0 42.1 1.0 HD11 A:ILE102 4.1 45.6 1.0 C5 A:Q4G301 4.1 20.2 0.5 HD2 A:TYR211 4.2 28.6 1.0 CE2 A:TYR211 4.3 28.5 1.0 H2 A:Q4G301 4.5 25.9 0.5 CD2 A:TYR211 4.6 23.8 1.0 C3 A:Q4G301 4.8 29.4 0.5 H5 A:Q4G301 4.9 31.7 0.5

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


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:81.1 occ:0.50 F B:Q4G301 0.0 81.1 0.5 C8 B:Q4G301 1.4 46.7 0.5 C7 B:Q4G301 2.3 32.3 0.5 C9 B:Q4G301 2.3 21.0 0.5 H4 B:Q4G301 2.6 25.2 0.5 H3 B:Q4G301 2.6 38.9 0.5 O B:HOH587 2.9 34.1 1.0 C6 B:Q4G301 3.6 21.1 0.5 HE2 B:TYR211 3.6 39.4 1.0 C4 B:Q4G301 3.6 24.4 0.5 O B:HOH528 3.7 38.8 1.0 HD11 B:ILE102 4.1 40.8 1.0 C5 B:Q4G301 4.1 23.7 0.5 CE2 B:TYR211 4.3 32.8 1.0 HD2 B:TYR211 4.3 34.7 1.0 H2 B:Q4G301 4.5 25.4 0.5 CD2 B:TYR211 4.6 28.8 1.0 O B:HOH476 4.7 40.9 1.0 O B:HOH578 4.7 32.2 1.0 H5 B:Q4G301 4.7 23.1 0.5 C3 B:Q4G301 4.8 25.6 0.5 HG21 B:THR213 4.9 37.2 1.0 HG1 B:THR213 5.0 24.9 1.0

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


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:85.7 occ:0.50 F C:Q4G301 0.0 85.7 0.5 C8 C:Q4G301 1.4 48.1 0.5 C7 C:Q4G301 2.3 26.6 0.5 C9 C:Q4G301 2.3 33.7 0.5 H4 C:Q4G301 2.6 40.6 0.5 H3 C:Q4G301 2.6 32.0 0.5 C6 C:Q4G301 3.6 25.0 0.5 C4 C:Q4G301 3.6 19.2 0.5 HE2 C:TYR211 3.7 25.6 1.0 HD11 C:ILE102 3.8 65.2 1.0 C5 C:Q4G301 4.1 20.7 0.5 HD2 C:TYR211 4.4 33.4 1.0 CE2 C:TYR211 4.4 21.3 1.0 HG21 C:THR213 4.4 47.5 1.0 H2 C:Q4G301 4.5 30.1 0.5 HG1 C:THR213 4.5 38.0 1.0 CD2 C:TYR211 4.7 27.7 1.0 CD1 C:ILE102 4.8 54.3 1.0 C3 C:Q4G301 4.8 32.7 0.5 H5 C:Q4G301 4.9 30.9 0.5

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


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 8B within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:57.2 occ:0.50 F D:Q4G301 0.0 57.2 0.5 C8 D:Q4G301 1.4 40.8 0.5 C7 D:Q4G301 2.3 26.5 0.5 C9 D:Q4G301 2.3 23.0 0.5 H4 D:Q4G301 2.6 27.6 0.5 H3 D:Q4G301 2.6 31.9 0.5 HE2 D:TYR211 3.0 44.4 1.0 HD2 D:TYR211 3.5 32.5 1.0 C6 D:Q4G301 3.6 24.7 0.5 C4 D:Q4G301 3.6 26.0 0.5 CE2 D:TYR211 3.7 36.9 1.0 HD11 D:ILE102 3.9 62.1 1.0 CD2 D:TYR211 4.0 27.1 1.0 C5 D:Q4G301 4.1 25.5 0.5 HG21 D:THR213 4.3 75.3 1.0 H2 D:Q4G301 4.5 29.7 0.5 HH D:TYR211 4.7 76.4 1.0 HG1 D:THR213 4.8 46.5 1.0 C3 D:Q4G301 4.8 32.5 0.5 HB3 D:SER244 4.8 49.3 1.0 CZ D:TYR211 4.8 45.7 1.0 CD1 D:ILE102 4.9 51.7 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