Fluorine in PDB 6yd1: Saftsz-Dfmba

The structure of Saftsz-Dfmba, PDB code: 6yd1 was solved by C.Fernandez-Tornero, F.M.Ruiz, J.M.Andreu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.15 / 1.70
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.334, 51.139, 87.823, 90, 110.44, 90
R / Rfree (%)	17.2 / 21.9

The structure of Saftsz-Dfmba also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Fluorine atom in the Saftsz-Dfmba (pdb code 6yd1). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Saftsz-Dfmba, PDB code: 6yd1:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Saftsz-Dfmba


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Saftsz-Dfmba within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:26.5 occ:0.65 FAF A:OLQ402 0.0 26.5 0.7 CAB A:OLQ402 1.4 27.0 0.7 CAC A:OLQ402 2.4 32.3 0.7 CAI A:OLQ402 2.4 29.0 0.7 OAL A:OLQ402 2.7 28.8 0.7 HAP A:OLQ402 2.8 18.9 0.7 CAG A:OLQ402 2.8 30.8 0.7 NAA A:OLQ402 3.0 15.8 0.7 OD1 A:ASN263 3.0 33.0 1.0 CG A:ASN263 3.2 33.4 1.0 CB A:ASN263 3.2 26.5 1.0 CD1 A:LEU209 3.4 27.0 1.0 CAD A:OLQ402 3.6 27.6 0.7 CB A:LEU209 3.6 25.7 1.0 CAJ A:OLQ402 3.7 27.7 0.7 CD1 A:LEU200 3.7 34.3 1.0 HAA A:OLQ402 3.7 18.9 0.7 CG A:LEU209 3.7 27.2 1.0 CG A:LEU200 3.7 40.5 1.0 OAH A:OLQ402 3.7 30.1 0.7 CAM A:OLQ402 4.1 30.7 0.7 CAE A:OLQ402 4.2 25.7 0.7 CB A:LEU200 4.2 33.5 1.0 ND2 A:ASN263 4.2 29.4 1.0 HAJ A:OLQ402 4.4 33.2 0.7 HAN A:OLQ402 4.4 36.8 0.7 CA A:ASN263 4.4 23.3 1.0 HAM A:OLQ402 4.5 36.8 0.7 HAO A:OLQ402 4.6 36.8 0.7 FAK A:OLQ402 4.7 30.2 0.7 CA A:LEU200 4.7 32.7 1.0 CD2 A:LEU261 4.7 30.6 1.0 CA A:LEU209 4.7 21.4 1.0 N A:LEU209 4.7 24.8 1.0 CA A:GLY295 4.8 24.0 1.0

Fluorine binding site 2 out of 2 in the Saftsz-Dfmba


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Saftsz-Dfmba within 5.0Å range: probe atom residue distance (Å) B Occ A:F402 b:30.2 occ:0.65 FAK A:OLQ402 0.0 30.2 0.7 CAD A:OLQ402 1.3 27.6 0.7 CAC A:OLQ402 2.3 32.3 0.7 CAE A:OLQ402 2.4 25.7 0.7 HAE A:OLQ402 2.6 30.8 0.7 CAG A:OLQ402 2.7 30.8 0.7 CG2 A:VAL297 2.9 29.5 1.0 OAH A:OLQ402 2.9 30.1 0.7 O A:VAL203 3.0 34.4 1.0 CG1 A:VAL203 3.2 31.1 1.0 CB A:VAL203 3.3 34.2 1.0 C A:VAL203 3.5 35.5 1.0 CAB A:OLQ402 3.6 27.0 0.7 CAJ A:OLQ402 3.6 27.7 0.7 NAA A:OLQ402 3.7 15.8 0.7 K A:K403 3.7 28.3 1.0 N A:GLY205 3.8 26.2 1.0 HAP A:OLQ402 3.9 18.9 0.7 CA A:VAL203 4.0 37.1 1.0 CA A:GLY205 4.1 28.7 1.0 CAI A:OLQ402 4.1 29.0 0.7 C A:SER204 4.1 32.1 1.0 CB A:VAL297 4.2 32.2 1.0 HAA A:OLQ402 4.2 18.9 0.7 N A:SER204 4.2 32.5 1.0 O A:ASP199 4.3 34.1 1.0 O A:HOH658 4.4 46.5 1.0 O A:LEU200 4.4 35.7 1.0 HAJ A:OLQ402 4.4 33.2 0.7 O A:SER204 4.5 35.7 1.0 CA A:LEU200 4.5 32.7 1.0 CG1 A:VAL297 4.5 26.2 1.0 CA A:SER204 4.5 36.0 1.0 N A:VAL203 4.6 32.2 1.0 CG2 A:VAL203 4.6 34.8 1.0 OD1 A:ASN208 4.6 26.3 1.0 FAF A:OLQ402 4.7 26.5 0.7 C A:LEU200 4.8 39.6 1.0 OD1 A:ASN263 4.9 33.0 1.0 C A:ASP199 5.0 30.9 1.0

S.Huecas, L.Araujo-Bazan, F.M.Ruiz, L.B.Ruiz-Avila, R.F.Martinez, A.Escobar-Pena, M.Artola, H.Vazquez-Villa, M.Martin-Fontecha, C.Fernandez-Tornero, M.L.Lopez-Rodriguez, J.M.Andreu. Targeting the Ftsz Allosteric Binding Site with A Novel Fluorescence Polarization Screen, Cytological and Structural Approaches For Antibacterial Discovery. J.Med.Chem. V. 64 5730 2021.
ISSN: ISSN 0022-2623
PubMed: 33908781
DOI: 10.1021/ACS.JMEDCHEM.0C02207