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Fluorine in PDB 6yd6: Saftsz-UCM152 (Comp.20)

Protein crystallography data

The structure of Saftsz-UCM152 (Comp.20), PDB code: 6yd6 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) 40.16 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 71.744, 50.184, 88.374, 90, 111.06, 90
R / Rfree (%) 16.5 / 20

Other elements in 6yd6:

The structure of Saftsz-UCM152 (Comp.20) also contains other interesting chemical elements:

Potassium (K) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Saftsz-UCM152 (Comp.20) (pdb code 6yd6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Saftsz-UCM152 (Comp.20), PDB code: 6yd6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 6yd6

Go back to Fluorine Binding Sites List in 6yd6
Fluorine binding site 1 out of 5 in the Saftsz-UCM152 (Comp.20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Saftsz-UCM152 (Comp.20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:30.9
occ:1.00
 F A:OMW402 0.0 30.9 1.0
C2 A:OMW402 1.4 26.1 1.0
C1 A:OMW402 2.4 24.3 1.0
C3 A:OMW402 2.4 24.5 1.0
C A:OMW402 2.8 31.1 1.0
O A:OMW402 2.9 30.6 1.0
CG2 A:VAL297 3.0 27.1 1.0
CG1 A:VAL203 3.2 34.2 1.0
O A:VAL203 3.3 32.2 1.0
CB A:VAL203 3.3 30.0 1.0
C14 A:OMW402 3.6 26.3 1.0
C A:VAL203 3.6 32.6 1.0
C4 A:OMW402 3.7 24.1 1.0
K A:K403 3.8 29.9 1.0
N A:GLY205 3.8 26.5 1.0
N A:OMW402 3.9 22.8 1.0
CA A:VAL203 4.0 31.0 1.0
CA A:GLY205 4.1 28.2 1.0
C5 A:OMW402 4.1 25.2 1.0
C A:SER204 4.2 36.1 1.0
O A:ASP199 4.3 27.9 1.0
CB A:VAL297 4.3 28.0 1.0
N A:SER204 4.3 36.5 1.0
O A:LEU200 4.5 28.8 1.0
CG1 A:VAL297 4.5 27.1 1.0
CG2 A:VAL203 4.5 35.2 1.0
CA A:LEU200 4.6 23.1 1.0
CA A:SER204 4.6 35.6 0.6
O A:SER204 4.6 42.0 1.0
CA A:SER204 4.7 35.6 0.4
N A:VAL203 4.7 30.8 1.0
F1 A:OMW402 4.7 25.9 1.0
O A:HOH655 4.8 46.7 1.0
OD1 A:ASN208 4.8 31.5 1.0
C A:LEU200 5.0 28.2 1.0

Fluorine binding site 2 out of 5 in 6yd6

Go back to Fluorine Binding Sites List in 6yd6
Fluorine binding site 2 out of 5 in the Saftsz-UCM152 (Comp.20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Saftsz-UCM152 (Comp.20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:25.9
occ:1.00
 F1 A:OMW402 0.0 25.9 1.0
C14 A:OMW402 1.4 26.3 1.0
C1 A:OMW402 2.4 24.3 1.0
C5 A:OMW402 2.4 25.2 1.0
O1 A:OMW402 2.7 26.2 1.0
C A:OMW402 2.8 31.1 1.0
N A:OMW402 3.0 22.8 1.0
OD1 A:ASN263 3.2 26.7 1.0
CB A:ASN263 3.3 24.7 1.0
CG A:ASN263 3.3 28.0 1.0
CD1 A:LEU209 3.5 24.3 1.0
CD1 A:LEU200 3.6 30.6 1.0
CB A:LEU209 3.6 25.3 1.0
CG A:LEU209 3.6 22.0 1.0
C2 A:OMW402 3.6 26.1 1.0
C4 A:OMW402 3.7 24.1 1.0
O A:OMW402 3.7 30.6 1.0
CG A:LEU200 3.8 27.8 1.0
C6 A:OMW402 4.1 29.5 1.0
C3 A:OMW402 4.2 24.5 1.0
ND2 A:ASN263 4.2 24.2 1.0
CB A:LEU200 4.4 26.7 1.0
C13 A:OMW402 4.4 31.8 1.0
CA A:ASN263 4.6 21.5 1.0
CD2 A:LEU261 4.6 29.3 1.0
CA A:LEU209 4.7 24.5 1.0
F A:OMW402 4.7 30.9 1.0
C7 A:OMW402 4.8 27.9 1.0
N A:LEU209 4.8 26.4 1.0
CA A:LEU200 4.8 23.1 1.0
CA A:GLY295 5.0 23.2 1.0

Fluorine binding site 3 out of 5 in 6yd6

Go back to Fluorine Binding Sites List in 6yd6
Fluorine binding site 3 out of 5 in the Saftsz-UCM152 (Comp.20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Saftsz-UCM152 (Comp.20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:39.6
occ:1.00
 F2 A:OMW402 0.0 39.6 1.0
C10 A:OMW402 1.4 41.5 1.0
F4 A:OMW402 2.2 34.9 1.0
F3 A:OMW402 2.2 36.9 1.0
C9 A:OMW402 2.4 31.5 1.0
C8 A:OMW402 2.9 31.5 1.0
O A:GLN192 3.4 27.5 1.0
C11 A:OMW402 3.5 35.3 1.0
O A:HOH578 3.5 32.3 1.0
CA A:GLY196 3.6 23.7 1.0
CG2 A:THR309 3.8 27.5 1.0
O A:GLY227 3.9 26.6 1.0
CB A:THR309 4.1 30.9 1.0
C A:GLN192 4.2 25.4 1.0
C7 A:OMW402 4.2 27.9 1.0
N A:GLY196 4.3 21.3 1.0
CA A:GLY193 4.4 22.8 1.0
C A:GLY227 4.5 33.8 1.0
C A:GLY196 4.5 28.1 1.0
CB A:ILE228 4.6 34.9 1.0
N A:GLY193 4.7 21.9 1.0
C12 A:OMW402 4.7 28.5 1.0
O A:GLY193 4.8 26.6 1.0
N A:GLY227 4.8 25.5 1.0
C13 A:OMW402 4.9 31.8 1.0
CA A:THR309 5.0 21.6 1.0

Fluorine binding site 4 out of 5 in 6yd6

Go back to Fluorine Binding Sites List in 6yd6
Fluorine binding site 4 out of 5 in the Saftsz-UCM152 (Comp.20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Saftsz-UCM152 (Comp.20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:36.9
occ:1.00
 F3 A:OMW402 0.0 36.9 1.0
C10 A:OMW402 1.4 41.5 1.0
F4 A:OMW402 2.2 34.9 1.0
F2 A:OMW402 2.2 39.6 1.0
C9 A:OMW402 2.4 31.5 1.0
C8 A:OMW402 3.0 31.5 1.0
O A:GLY193 3.1 26.6 1.0
C11 A:OMW402 3.4 35.3 1.0
CA A:GLY193 3.5 22.8 1.0
CA A:GLY196 3.5 23.7 1.0
O A:GLN192 3.6 27.5 1.0
C A:GLY193 3.7 30.9 1.0
N A:ILE197 3.7 23.7 1.0
C A:GLY196 3.8 28.1 1.0
CE A:MET226 3.8 31.5 1.0
N A:GLY196 4.1 21.3 1.0
CG1 A:ILE197 4.2 26.6 1.0
C7 A:OMW402 4.3 27.9 1.0
N A:GLY193 4.4 21.9 1.0
C A:GLN192 4.4 25.4 1.0
CD1 A:ILE197 4.4 31.1 1.0
CB A:MET226 4.6 27.0 1.0
C12 A:OMW402 4.6 28.5 1.0
O A:GLY196 4.6 27.1 1.0
CA A:ILE197 4.7 21.9 1.0
CG1 A:ILE311 4.7 32.9 1.0
CG A:MET226 4.8 26.9 1.0
SD A:MET226 4.8 31.7 1.0
C13 A:OMW402 4.9 31.8 1.0
O A:HOH578 5.0 32.3 1.0
CD1 A:ILE311 5.0 34.2 1.0
N A:VAL194 5.0 26.1 1.0

Fluorine binding site 5 out of 5 in 6yd6

Go back to Fluorine Binding Sites List in 6yd6
Fluorine binding site 5 out of 5 in the Saftsz-UCM152 (Comp.20)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Saftsz-UCM152 (Comp.20) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:34.9
occ:1.00
 F4 A:OMW402 0.0 34.9 1.0
C10 A:OMW402 1.4 41.5 1.0
F2 A:OMW402 2.2 39.6 1.0
F3 A:OMW402 2.2 36.9 1.0
C9 A:OMW402 2.4 31.5 1.0
C11 A:OMW402 2.8 35.3 1.0
N A:GLY227 3.4 25.5 1.0
CB A:MET226 3.5 27.0 1.0
O A:VAL310 3.5 25.0 1.0
CA A:MET226 3.6 22.4 1.0
C A:MET226 3.6 30.4 1.0
O A:GLY227 3.6 26.6 1.0
C8 A:OMW402 3.7 31.5 1.0
CG A:MET226 4.1 26.9 1.0
C12 A:OMW402 4.2 28.5 1.0
CG1 A:ILE311 4.2 32.9 1.0
C A:VAL310 4.2 23.7 1.0
C A:GLY227 4.2 33.8 1.0
CA A:GLY227 4.4 35.6 1.0
O A:MET226 4.4 33.2 1.0
CA A:GLY193 4.5 22.8 1.0
N A:VAL310 4.5 23.0 1.0
CE A:MET226 4.5 31.5 1.0
O A:GLN192 4.7 27.5 1.0
CB A:THR309 4.8 30.9 1.0
C7 A:OMW402 4.8 27.9 1.0
N A:ILE311 4.8 24.4 1.0
SD A:MET226 5.0 31.7 1.0
C13 A:OMW402 5.0 31.8 1.0

Reference:

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
Page generated: Tue Jul 15 17:40:57 2025

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