Fluorine in PDB 5onl: Yndl-Apo (Zinc-Free)

The structure of Yndl-Apo (Zinc-Free), PDB code: 5onl was solved by S.Ramaswamy, M.Rasheed, C.Morelli, C.Calvio, B.Sutton, A.Pastore, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.75 / 1.70
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	38.612, 47.284, 99.893, 90.00, 90.00, 90.00
R / Rfree (%)	17.4 / 21.2

The binding sites of Fluorine atom in the Yndl-Apo (Zinc-Free) (pdb code 5onl). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Yndl-Apo (Zinc-Free), PDB code: 5onl:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Yndl-Apo (Zinc-Free)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Yndl-Apo (Zinc-Free) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:20.1 occ:0.50 F A:FAH303 0.0 20.1 0.5 F A:FAH303 0.9 22.4 0.5 CH3 A:FAH303 1.4 22.2 0.5 CH3 A:FAH303 1.9 23.6 0.5 C A:FAH303 2.3 21.9 0.5 OG A:SER80 2.7 11.4 1.0 C A:FAH303 2.8 25.1 0.5 OXT A:FAH303 2.9 26.1 0.5 N A:SER80 3.0 10.6 1.0 O A:FAH303 3.1 22.6 0.5 NE2 A:HIS41 3.2 14.0 1.0 O A:FAH303 3.2 20.8 0.5 CB A:SER80 3.5 10.6 1.0 O A:HOH408 3.7 34.5 1.0 CA A:SER80 3.7 10.5 1.0 OXT A:FAH303 3.8 23.8 0.5 OG1 A:THR79 3.8 13.9 1.0 NE2 A:HIS102 3.8 23.4 1.0 CA A:THR79 3.8 12.8 1.0 C A:THR79 3.8 10.3 1.0 CD2 A:HIS41 4.0 11.3 1.0 CD2 A:HIS102 4.1 20.3 1.0 CE1 A:HIS41 4.1 11.0 1.0 O A:HOH468 4.4 18.6 1.0 O A:HOH409 4.4 39.1 1.0 CB A:THR79 4.5 12.4 1.0 CD1 A:ILE40 4.5 9.5 1.0 NE2 A:HIS77 4.6 15.2 1.0 CE1 A:HIS102 4.6 21.3 1.0 O A:ILE78 4.8 11.8 1.0 CE1 A:HIS77 4.9 15.7 1.0 N A:THR79 5.0 11.8 1.0 CG A:HIS102 5.0 15.8 1.0 O A:THR79 5.0 11.5 1.0

Fluorine binding site 2 out of 2 in the Yndl-Apo (Zinc-Free)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Yndl-Apo (Zinc-Free) within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:22.4 occ:0.50 F A:FAH303 0.0 22.4 0.5 CH3 A:FAH303 0.6 22.2 0.5 F A:FAH303 0.9 20.1 0.5 CH3 A:FAH303 1.4 23.6 0.5 C A:FAH303 1.8 21.9 0.5 C A:FAH303 2.4 25.1 0.5 O A:FAH303 2.6 22.6 0.5 OXT A:FAH303 2.7 26.1 0.5 O A:FAH303 2.7 20.8 0.5 OG A:SER80 3.3 11.4 1.0 N A:SER80 3.4 10.6 1.0 O A:HOH408 3.4 34.5 1.0 OG1 A:THR79 3.5 13.9 1.0 OXT A:FAH303 3.5 23.8 0.5 NE2 A:HIS41 3.8 14.0 1.0 CB A:SER80 3.9 10.6 1.0 O A:HOH409 4.0 39.1 1.0 CA A:THR79 4.0 12.8 1.0 O A:HOH468 4.1 18.6 1.0 C A:THR79 4.2 10.3 1.0 CA A:SER80 4.3 10.5 1.0 NE2 A:HIS102 4.3 23.4 1.0 CB A:THR79 4.4 12.4 1.0 CD2 A:HIS102 4.5 20.3 1.0 CD2 A:HIS41 4.6 11.3 1.0 NE2 A:HIS77 4.6 15.2 1.0 CE1 A:HIS41 4.8 11.0 1.0 CE1 A:HIS77 4.8 15.7 1.0 CE1 A:HIS102 4.9 21.3 1.0

S.Ramaswamy, M.Rasheed, C.Morelli, C.Calvio, B.Sutton, A.Pastore. Poly-Gamma-Glutamate Hydrolases Structure: A Potential Strategy Against Staphylococcus Infectivity To Be Published.