Fluorine in PDB 5cy7: Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275

All present enzymatic activity of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275:
3.5.1.88;

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275, PDB code: 5cy7 was solved by H.P.T.Ngo, L.W.Kang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.40 / 2.40
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	58.823, 58.823, 264.034, 90.00, 90.00, 120.00
R / Rfree (%)	18.1 / 21.2

The structure of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 also contains other interesting chemical elements:

Cadmium	(Cd)	3 atoms
Sodium	(Na)	1 atom

The binding sites of Fluorine atom in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 (pdb code 5cy7). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275, PDB code: 5cy7:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 within 5.0Å range: probe atom residue distance (Å) B Occ A:F205 b:66.2 occ:1.00 F12 A:56U205 0.0 66.2 1.0 C10 A:56U205 1.4 61.3 1.0 F11 A:56U205 2.2 66.8 1.0 C8 A:56U205 2.3 59.3 1.0 O A:HOH302 2.9 31.4 1.0 CD A:ARG68 3.0 48.8 1.0 N9 A:56U205 3.1 57.8 1.0 N7 A:56U205 3.2 59.8 1.0 NE A:ARG68 3.3 49.8 1.0 CD2 A:LEU100 3.9 22.6 1.0 CZ A:ARG68 3.9 53.2 1.0 CA A:GLY44 4.2 22.2 1.0 NH1 A:ARG68 4.2 53.5 1.0 C3 A:56U205 4.2 60.8 1.0 C2 A:56U205 4.3 57.0 1.0 CG A:LEU100 4.3 22.8 1.0 CG A:ARG68 4.4 51.5 1.0 O A:HIS43 4.4 28.8 1.0 N A:VAL45 4.5 19.4 1.0 CE1 A:TYR69 4.5 49.9 1.0 NH2 A:ARG68 4.7 49.7 1.0 C A:GLY44 4.8 21.1 1.0 N A:CYS99 4.8 26.2 1.0 CB A:ARG68 4.8 59.4 1.0 OH A:TYR69 4.8 59.0 1.0 N A:LEU100 4.9 24.5 1.0

Fluorine binding site 2 out of 2 in the Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 within 5.0Å range: probe atom residue distance (Å) B Occ A:F205 b:66.8 occ:1.00 F11 A:56U205 0.0 66.8 1.0 C10 A:56U205 1.4 61.3 1.0 F12 A:56U205 2.2 66.2 1.0 C8 A:56U205 2.4 59.3 1.0 N7 A:56U205 2.8 59.8 1.0 N A:CYS99 3.3 26.2 1.0 C A:GLY98 3.4 27.0 1.0 CA A:GLY98 3.5 24.5 1.0 N9 A:56U205 3.7 57.8 1.0 OH A:TYR69 3.9 59.0 1.0 CD A:ARG68 3.9 48.8 1.0 N A:GLY98 4.0 24.9 1.0 O A:GLY98 4.1 29.3 1.0 C2 A:56U205 4.1 57.0 1.0 CA A:CYS99 4.2 24.1 1.0 NH1 A:ARG68 4.3 53.5 1.0 NE A:ARG68 4.4 49.8 1.0 C A:CYS99 4.5 23.7 1.0 C3 A:56U205 4.5 60.8 1.0 O A:HOH302 4.6 31.4 1.0 CZ A:ARG68 4.6 53.2 1.0 CZ A:TYR69 4.7 56.3 1.0 CE1 A:TYR69 4.7 49.9 1.0 N A:LEU100 4.8 24.5 1.0 O A:CYS99 4.9 21.7 1.0

H.P.T.Ngo, L.W.Kang. Structure of XOO1075, A Peptide Deformylase From Xanthomonas Oryze Pv Oryze, in Complex with Fragment 275 To Be Published.