Fluorine in PDB 5oxd: Complex of A C. Perfringens O-Glcnacase with A Fragment Hit

All present enzymatic activity of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit:
3.2.1.169; 3.2.1.52;

The structure of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit, PDB code: 5oxd was solved by K.Rafie, D.M.F.Van Aalten, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	50.01 / 2.60
Space group	P 61
Cell size a, b, c (Å), α, β, γ (°)	117.794, 117.794, 147.233, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 22.1

The structure of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit also contains other interesting chemical elements:

Cadmium

(Cd)

22 atoms

The binding sites of Fluorine atom in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit (pdb code 5oxd). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit, PDB code: 5oxd:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range: probe atom residue distance (Å) B Occ A:F723 b:0.8 occ:1.00 FAI A:B2W723 0.0 0.8 1.0 CAH A:B2W723 1.5 0.9 1.0 FAJ A:B2W723 2.2 0.2 1.0 CAF A:B2W723 2.4 0.9 1.0 FAK A:B2W723 2.5 0.1 1.0 NAE A:B2W723 2.8 0.3 1.0 CAG A:B2W723 3.6 0.7 1.0 CAD A:B2W723 4.2 0.3 1.0 CAC A:B2W723 4.8 0.5 1.0 CAA A:B2W723 4.8 97.2 1.0

Fluorine binding site 2 out of 3 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range: probe atom residue distance (Å) B Occ A:F723 b:0.2 occ:1.00 FAJ A:B2W723 0.0 0.2 1.0 CAH A:B2W723 1.3 0.9 1.0 FAI A:B2W723 2.2 0.8 1.0 CAF A:B2W723 2.3 0.9 1.0 FAK A:B2W723 2.3 0.1 1.0 NAE A:B2W723 2.8 0.3 1.0 CAG A:B2W723 3.3 0.7 1.0 OH A:TYR189 3.4 70.3 1.0 CZ A:TYR189 3.4 75.1 1.0 CE2 A:TYR189 3.7 77.2 1.0 CE1 A:TYR189 3.9 73.4 1.0 CAD A:B2W723 4.2 0.3 1.0 CD2 A:TYR189 4.5 69.6 1.0 CAA A:B2W723 4.6 97.2 1.0 CD1 A:TYR189 4.7 73.4 1.0 CG A:TYR189 4.9 65.8 1.0

Fluorine binding site 3 out of 3 in the Complex of A C. Perfringens O-Glcnacase with A Fragment Hit


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Complex of A C. Perfringens O-Glcnacase with A Fragment Hit within 5.0Å range: probe atom residue distance (Å) B Occ A:F723 b:0.1 occ:1.00 FAK A:B2W723 0.0 0.1 1.0 CAH A:B2W723 1.5 0.9 1.0 FAJ A:B2W723 2.3 0.2 1.0 CAF A:B2W723 2.5 0.9 1.0 FAI A:B2W723 2.5 0.8 1.0 CAG A:B2W723 2.7 0.7 1.0 NAE A:B2W723 3.7 0.3 1.0 CAA A:B2W723 4.1 97.2 1.0 CE2 A:TYR189 4.4 77.2 1.0 CD2 A:TYR189 4.6 69.6 1.0 CZ A:TYR189 4.7 75.1 1.0

V.S.Borodkin, K.Rafie, N.Selvan, T.Aristotelous, I.Navratilova, A.T.Ferenbach, D.M.F.Van Aalten. O-Glcnacase Fragment Discovery with Fluorescence Polarimetry. Acs Chem. Biol. V. 13 1353 2018.
ISSN: ESSN 1554-8937
PubMed: 29641181
DOI: 10.1021/ACSCHEMBIO.8B00183