Fluorine in PDB 6v1o: Structure of Oxa-48 Bound to QPX7728 at 1.80 A

All present enzymatic activity of Structure of Oxa-48 Bound to QPX7728 at 1.80 A:
3.5.2.6;

The structure of Structure of Oxa-48 Bound to QPX7728 at 1.80 A, PDB code: 6v1o was solved by O.A.Pemberton, Y.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.85 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	58.440, 105.550, 94.403, 90.00, 107.92, 90.00
R / Rfree (%)	15.8 / 22.4

The structure of Structure of Oxa-48 Bound to QPX7728 at 1.80 A also contains other interesting chemical elements:

Magnesium	(Mg)	8 atoms
Chlorine	(Cl)	2 atoms

The binding sites of Fluorine atom in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A (pdb code 6v1o). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A, PDB code: 6v1o:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:11.5 occ:0.94 F06 A:RM9301 0.0 11.5 0.9 C05 A:RM9301 1.3 10.9 0.9 C04 A:RM9301 2.4 9.1 0.9 C07 A:RM9301 2.4 11.9 0.9 C02 A:RM9301 2.8 9.7 0.9 O03 A:RM9301 3.2 9.8 0.9 NH1 A:ARG250 3.4 10.1 1.0 O01 A:RM9301 3.5 8.9 0.9 CD1 A:LEU247 3.6 10.5 1.0 C10 A:RM9301 3.7 8.8 0.9 C08 A:RM9301 3.7 11.2 0.9 O A:HOH708 3.7 34.5 1.0 NH2 A:ARG250 3.9 11.5 1.0 CZ A:ARG250 4.1 9.5 1.0 O A:HOH522 4.1 16.7 1.0 C09 A:RM9301 4.2 9.8 0.9 O A:HOH621 4.6 24.1 1.0 CB A:TYR211 4.6 9.2 1.0 CG A:LEU247 4.6 12.2 1.0 CD2 A:LEU247 4.7 13.1 1.0 O11 A:RM9301 4.8 7.8 0.9 CD2 A:TYR211 4.8 14.5 1.0 O A:HOH782 4.8 37.2 1.0 CB A:LEU247 4.9 11.3 1.0

Fluorine binding site 2 out of 4 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:16.3 occ:1.00 F06 B:RM9301 0.0 16.3 1.0 C05 B:RM9301 1.3 13.5 1.0 C04 B:RM9301 2.4 11.8 1.0 C07 B:RM9301 2.4 13.9 1.0 C02 B:RM9301 2.8 13.9 1.0 O01 B:RM9301 3.1 15.1 1.0 NH1 B:ARG250 3.3 7.3 1.0 O03 B:RM9301 3.4 13.2 1.0 C08 B:RM9301 3.6 13.5 1.0 C10 B:RM9301 3.6 10.4 1.0 NH2 B:ARG250 3.7 7.9 1.0 CD1 B:LEU247 3.7 11.8 1.0 CZ B:ARG250 3.9 8.0 1.0 C09 B:RM9301 4.1 12.4 1.0 O B:HOH482 4.2 27.8 1.0 O B:HOH679 4.4 43.6 1.0 CB B:TYR211 4.4 8.6 1.0 CD2 B:LEU247 4.4 12.1 1.0 CG B:LEU247 4.5 11.6 1.0 O11 B:RM9301 4.7 9.8 1.0 CB B:LEU247 4.9 10.6 1.0 OG1 B:THR209 4.9 9.4 1.0

Fluorine binding site 3 out of 4 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:20.5 occ:1.00 F06 C:RM9301 0.0 20.5 1.0 C05 C:RM9301 1.3 19.3 1.0 C04 C:RM9301 2.4 18.3 1.0 C07 C:RM9301 2.4 19.6 1.0 C02 C:RM9301 2.8 19.7 1.0 O01 C:RM9301 3.2 20.3 1.0 NH1 C:ARG250 3.2 11.5 1.0 O03 C:RM9301 3.5 20.4 1.0 CD1 C:LEU247 3.6 14.7 1.0 C10 C:RM9301 3.6 16.7 1.0 C08 C:RM9301 3.6 17.9 1.0 NH2 C:ARG250 3.7 14.4 1.0 CZ C:ARG250 3.9 12.7 1.0 C09 C:RM9301 4.2 16.3 1.0 CD2 C:LEU247 4.2 15.6 1.0 O C:HOH413 4.3 26.2 1.0 CB C:TYR211 4.3 14.3 1.0 CG C:LEU247 4.4 14.0 1.0 O11 C:RM9301 4.7 15.5 1.0 CB C:LEU247 4.8 13.5 1.0 CD2 C:TYR211 4.8 20.2 1.0 O C:HOH714 4.9 50.7 1.0 CG C:TYR211 5.0 18.6 1.0

Fluorine binding site 4 out of 4 in the Structure of Oxa-48 Bound to QPX7728 at 1.80 A


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of Oxa-48 Bound to QPX7728 at 1.80 A within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:10.8 occ:0.90 F06 D:RM9301 0.0 10.8 0.9 C05 D:RM9301 1.3 11.2 0.9 C07 D:RM9301 2.4 11.8 0.9 C04 D:RM9301 2.4 10.3 0.9 C02 D:RM9301 2.9 11.9 0.9 O D:HOH680 3.2 47.2 1.0 O03 D:RM9301 3.2 13.5 0.9 O D:HOH643 3.2 48.4 1.0 NH1 D:ARG250 3.3 12.5 1.0 O D:HOH721 3.5 45.7 1.0 C08 D:RM9301 3.6 11.4 0.9 O01 D:RM9301 3.6 11.8 0.9 C10 D:RM9301 3.7 7.5 0.9 CD1 D:LEU247 3.7 12.1 1.0 NH2 D:ARG250 3.8 13.6 1.0 CZ D:ARG250 4.0 13.4 1.0 C09 D:RM9301 4.2 9.4 0.9 O D:HOH531 4.3 16.3 1.0 CB D:TYR211 4.4 10.3 1.0 CD2 D:LEU247 4.5 11.1 1.0 CG D:LEU247 4.6 11.3 1.0 O11 D:RM9301 4.8 7.2 0.9 CD2 D:TYR211 4.9 16.6 1.0 OG1 D:THR209 5.0 9.6 1.0 CB D:LEU247 5.0 11.9 1.0 CG D:TYR211 5.0 14.2 1.0

S.J.Hecker, K.R.Reddy, O.Lomovskaya, D.C.Griffith, D.Rubio-Aparicio, K.Nelson, R.Tsivkovski, D.Sun, M.Sabet, Z.Tarazi, J.Parkinson, M.Totrov, S.H.Boyer, T.W.Glinka, O.A.Pemberton, Y.Chen, M.N.Dudley. Discovery of Cyclic Boronic Acid QPX7728, An Ultra-Broad-Spectrum Inhibitor of Serine and Metallo Beta-Lactamases. J.Med.Chem. 2020.
ISSN: ISSN 0022-2623
PubMed: 32150407
DOI: 10.1021/ACS.JMEDCHEM.9B01976