Fluorine in PDB 6yd5: Saftsz-UCM151 (Comp. 18)

The structure of Saftsz-UCM151 (Comp. 18), PDB code: 6yd5 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)	41.22 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	72.404, 50.182, 88.6, 90, 111.49, 90
R / Rfree (%)	18.4 / 23.4

The structure of Saftsz-UCM151 (Comp. 18) also contains other interesting chemical elements:

Chlorine	(Cl)	1 atom
Potassium	(K)	1 atom

The binding sites of Fluorine atom in the Saftsz-UCM151 (Comp. 18) (pdb code 6yd5). 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-UCM151 (Comp. 18), PDB code: 6yd5:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Saftsz-UCM151 (Comp. 18)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Saftsz-UCM151 (Comp. 18) within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:26.8 occ:1.00 F A:OM8404 0.0 26.8 1.0 C2 A:OM8404 1.4 24.9 1.0 C1 A:OM8404 2.4 24.6 1.0 C3 A:OM8404 2.4 24.2 1.0 HG21 A:VAL297 2.5 28.2 1.0 HG12 A:VAL203 2.5 39.7 1.0 H31 A:OM8404 2.6 29.0 1.0 HB A:VAL203 2.6 39.1 1.0 HG22 A:VAL297 2.7 28.2 1.0 C A:OM8404 2.8 25.6 1.0 O A:OM8404 2.9 27.2 1.0 CG2 A:VAL297 3.0 23.5 1.0 O A:VAL203 3.1 31.1 1.0 CG1 A:VAL203 3.1 33.1 1.0 CB A:VAL203 3.3 32.6 1.0 HG11 A:VAL203 3.3 39.7 1.0 HG23 A:VAL297 3.4 28.2 1.0 C A:VAL203 3.5 31.1 1.0 C13 A:OM8404 3.6 24.3 1.0 C4 A:OM8404 3.6 25.2 1.0 HA A:LEU200 3.7 31.7 1.0 HA3 A:GLY205 3.8 32.7 1.0 K A:K403 3.8 29.7 1.0 N A:GLY205 3.9 28.5 1.0 N A:OM8404 3.9 23.6 1.0 H A:GLY205 3.9 34.2 1.0 HA2 A:GLY205 4.0 32.7 1.0 CA A:VAL203 4.0 31.2 1.0 HG11 A:VAL297 4.0 28.4 1.0 HG13 A:VAL203 4.0 39.7 1.0 CA A:GLY205 4.1 27.2 1.0 C A:SER204 4.1 32.9 1.0 C5 A:OM8404 4.1 25.7 1.0 HN2 A:OM8404 4.2 28.3 1.0 N A:SER204 4.3 32.0 1.0 H A:VAL203 4.3 36.3 1.0 CB A:VAL297 4.3 23.0 1.0 O A:ASP199 4.3 29.0 1.0 H41 A:OM8404 4.4 30.2 1.0 HN3 A:OM8404 4.4 28.3 1.0 CG1 A:VAL297 4.5 23.7 1.0 O A:SER204 4.5 36.7 1.0 HG21 A:VAL203 4.5 39.1 1.0 HA A:SER204 4.5 40.1 0.6 O A:LEU200 4.5 25.5 1.0 CG2 A:VAL203 4.6 32.6 1.0 HA A:SER204 4.6 38.9 0.5 CA A:SER204 4.6 33.4 0.6 HG13 A:VAL297 4.6 28.4 1.0 CA A:SER204 4.6 32.4 0.5 N A:VAL203 4.6 30.3 1.0 CA A:LEU200 4.6 26.4 1.0 HB A:VAL297 4.7 27.6 1.0 OD1 A:ASN208 4.7 31.0 1.0 F1 A:OM8404 4.7 24.1 1.0 HA A:VAL203 4.8 37.4 1.0 O A:HOH505 4.9 50.0 1.0 H A:SER204 4.9 38.5 0.5 H A:SER204 4.9 38.5 0.6 C A:LEU200 5.0 25.2 1.0 HG23 A:VAL203 5.0 39.1 1.0

Fluorine binding site 2 out of 2 in the Saftsz-UCM151 (Comp. 18)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Saftsz-UCM151 (Comp. 18) within 5.0Å range: probe atom residue distance (Å) B Occ A:F404 b:24.1 occ:1.00 F1 A:OM8404 0.0 24.1 1.0 C13 A:OM8404 1.4 24.3 1.0 C5 A:OM8404 2.4 25.7 1.0 C1 A:OM8404 2.4 24.6 1.0 HD12 A:LEU209 2.4 32.4 1.0 HB2 A:ASN263 2.5 29.1 1.0 O1 A:OM8404 2.7 28.0 1.0 HN2 A:OM8404 2.8 28.3 1.0 C A:OM8404 2.9 25.6 1.0 HB2 A:LEU209 2.9 28.2 1.0 HD12 A:LEU200 3.0 32.4 1.0 N A:OM8404 3.0 23.6 1.0 HG A:LEU200 3.2 32.8 1.0 CD1 A:LEU209 3.2 27.0 1.0 CB A:ASN263 3.3 24.2 1.0 OD1 A:ASN263 3.3 25.8 1.0 HG A:LEU209 3.3 29.6 1.0 CG A:ASN263 3.4 26.4 1.0 HD11 A:LEU209 3.4 32.4 1.0 CG A:LEU209 3.6 24.7 1.0 HB3 A:ASN263 3.6 29.1 1.0 CD1 A:LEU200 3.6 27.0 1.0 C2 A:OM8404 3.6 24.9 1.0 C4 A:OM8404 3.6 25.2 1.0 CB A:LEU209 3.7 23.5 1.0 HD11 A:LEU200 3.7 32.4 1.0 H121 A:OM8404 3.7 43.1 1.0 HN3 A:OM8404 3.7 28.3 1.0 O A:OM8404 3.7 27.2 1.0 HD21 A:LEU261 3.8 36.4 1.0 CG A:LEU200 3.8 27.4 1.0 HB2 A:LEU200 4.0 31.6 1.0 HD13 A:LEU209 4.0 32.4 1.0 C6 A:OM8404 4.1 30.7 1.0 H A:LEU209 4.1 30.1 1.0 HA3 A:GLY295 4.1 25.2 1.0 C3 A:OM8404 4.1 24.2 1.0 HA A:LEU200 4.2 31.7 1.0 HB3 A:LEU209 4.2 28.2 1.0 ND2 A:ASN263 4.3 27.5 1.0 CB A:LEU200 4.4 26.3 1.0 H41 A:OM8404 4.4 30.2 1.0 H62 A:OM8404 4.4 36.9 1.0 HD23 A:LEU261 4.4 36.4 1.0 C12 A:OM8404 4.5 35.9 1.0 HD13 A:LEU200 4.5 32.4 1.0 CA A:ASN263 4.5 21.5 1.0 CD2 A:LEU261 4.5 30.4 1.0 HA A:ASN263 4.5 25.8 1.0 H61 A:OM8404 4.6 36.9 1.0 HD22 A:ASN263 4.7 33.0 1.0 HD21 A:ASN263 4.7 33.0 1.0 CA A:LEU209 4.7 22.6 1.0 N A:LEU209 4.7 25.1 1.0 F A:OM8404 4.7 26.8 1.0 C7 A:OM8404 4.8 34.1 1.0 CA A:LEU200 4.8 26.4 1.0 HG23 A:VAL297 4.9 28.2 1.0 HD22 A:LEU261 4.9 36.4 1.0 CA A:GLY295 5.0 21.0 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