Fluorine in PDB 6hrj: Apo - Yndl

The structure of Apo - Yndl, PDB code: 6hrj 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 (%)	17.7 / 21.3

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

Fluorine binding site 1 out of 2 in the Apo - Yndl


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Apo - Yndl within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:17.3 occ:0.50 F A:FAH303 0.0 17.3 0.5 F A:FAH303 1.0 23.3 0.5 CH3 A:FAH303 1.3 18.3 0.5 CH3 A:FAH303 1.7 23.1 0.5 C A:FAH303 2.4 17.8 0.5 OG A:SER80 2.7 11.6 1.0 OXT A:FAH303 2.7 21.9 0.5 C A:FAH303 2.9 24.0 0.5 N A:SER80 2.9 10.9 1.0 NE2 A:HIS41 3.1 13.6 1.0 O A:FAH303 3.4 21.0 0.5 O A:FAH303 3.4 19.9 0.5 CB A:SER80 3.5 10.7 1.0 OXT A:FAH303 3.7 22.6 0.5 CA A:THR79 3.7 12.5 1.0 CA A:SER80 3.7 10.7 1.0 C A:THR79 3.8 10.4 1.0 OG1 A:THR79 3.8 14.5 1.0 O A:HOH403 3.9 31.5 1.0 NE2 A:HIS102 3.9 22.5 1.0 CD2 A:HIS41 4.0 11.1 1.0 CE1 A:HIS41 4.1 10.9 1.0 CD2 A:HIS102 4.1 19.8 1.0 O A:HOH473 4.4 18.6 1.0 CB A:THR79 4.4 12.4 1.0 NE2 A:HIS77 4.5 14.4 1.0 CD1 A:ILE40 4.5 9.8 1.0 O A:HOH407 4.6 37.1 1.0 O A:ILE78 4.7 11.7 1.0 CE1 A:HIS102 4.7 20.6 1.0 CE1 A:HIS77 4.8 15.5 1.0 N A:THR79 4.9 11.7 1.0 O A:THR79 4.9 11.3 1.0

Fluorine binding site 2 out of 2 in the Apo - Yndl


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Apo - Yndl within 5.0Å range: probe atom residue distance (Å) B Occ A:F303 b:23.3 occ:0.50 F A:FAH303 0.0 23.3 0.5 CH3 A:FAH303 0.8 18.3 0.5 F A:FAH303 1.0 17.3 0.5 CH3 A:FAH303 1.3 23.1 0.5 C A:FAH303 2.1 17.8 0.5 C A:FAH303 2.4 24.0 0.5 OXT A:FAH303 2.6 21.9 0.5 O A:FAH303 2.6 21.0 0.5 O A:FAH303 3.1 19.9 0.5 OG A:SER80 3.2 11.6 1.0 O A:HOH403 3.3 31.5 1.0 OXT A:FAH303 3.5 22.6 0.5 N A:SER80 3.6 10.9 1.0 NE2 A:HIS41 3.8 13.6 1.0 OG1 A:THR79 3.8 14.5 1.0 CB A:SER80 3.9 10.7 1.0 NE2 A:HIS102 4.0 22.5 1.0 O A:HOH407 4.0 37.1 1.0 CD2 A:HIS102 4.2 19.8 1.0 O A:HOH473 4.3 18.6 1.0 CA A:THR79 4.3 12.5 1.0 CA A:SER80 4.3 10.7 1.0 C A:THR79 4.5 10.4 1.0 CD2 A:HIS41 4.5 11.1 1.0 CE1 A:HIS102 4.6 20.6 1.0 CB A:THR79 4.7 12.4 1.0 NE2 A:HIS77 4.8 14.4 1.0 CG A:HIS102 4.9 15.6 1.0 OE1 A:GLU165 4.9 28.1 1.0 CE1 A:HIS41 4.9 10.9 1.0

S.Ramaswamy, M.Rasheed, C.F.Morelli, C.Calvio, B.J.Sutton, A.Pastore. The Structure of Pghl Hydrolase Bound to Its Substrate Poly-Gamma-Glutamate. Febs J. V. 285 4575 2018.
ISSN: ISSN 1742-4658
PubMed: 30387270
DOI: 10.1111/FEBS.14688