Fluorine in PDB 5uv2: Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate, PDB code: 5uv2 was solved by R.Prem Kumar, K.Malik, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.20
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.699, 85.699, 214.880, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 23

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate also contains other interesting chemical elements:

Manganese

(Mn)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate (pdb code 5uv2). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate, PDB code: 5uv2:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:52.1 occ:0.46 F2 A:LA6704 0.0 52.1 0.5 C2 A:LA6704 1.3 53.2 0.5 C1 A:LA6704 2.2 54.2 0.5 C3 A:LA6704 2.3 53.4 0.5 C1 A:LA6704 2.5 54.8 0.5 C4 A:LA6704 2.7 51.9 0.5 O1 A:LA6704 2.8 54.6 0.5 O1 A:LA6704 2.9 54.8 0.5 OG1 A:THR340 3.2 48.2 1.0 C2 A:LA6704 3.3 53.6 0.5 CA A:THR340 3.6 40.7 1.0 C5 A:LA6704 3.7 55.0 0.5 CB A:THR340 3.8 41.6 1.0 F2 A:LA6704 3.9 59.8 0.5 C6 A:LA6704 4.0 50.8 0.5 CG2 A:THR340 4.0 46.4 1.0 C3 A:LA6704 4.1 54.0 0.5 N A:THR340 4.2 38.6 1.0 PA A:LA6704 4.3 49.4 0.5 C5 A:LA6704 4.3 51.9 0.5 PA A:LA6704 4.4 50.6 0.5 C9 A:LA6704 4.5 48.8 0.5 O3A A:LA6704 4.7 51.0 0.5 CG2 A:ILE339 4.7 41.2 1.0 OD2 A:ASP343 4.7 47.9 1.0 C A:THR340 4.8 42.1 1.0 C A:ILE339 4.8 38.0 1.0 O3A A:LA6704 4.8 51.0 0.5 O A:THR340 4.9 40.6 1.0 CB A:ASP343 4.9 42.6 1.0 C6 A:LA6704 4.9 49.3 0.5 O A:ILE339 4.9 40.6 1.0 O1A A:LA6704 4.9 51.7 0.5

Fluorine binding site 2 out of 2 in the Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of (+)-Limonene Synthase Complexed with 2- Fluoroneryl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:59.8 occ:0.54 F2 A:LA6704 0.0 59.8 0.5 C2 A:LA6704 1.3 53.6 0.5 C1 A:LA6704 1.9 54.8 0.5 C3 A:LA6704 2.3 54.0 0.5 C1 A:LA6704 2.5 54.2 0.5 C4 A:LA6704 2.7 50.2 0.5 C5 A:LA6704 2.8 55.0 0.5 O1 A:LA6704 2.8 54.6 0.5 C2 A:LA6704 2.8 53.2 0.5 O1 A:LA6704 3.2 54.8 0.5 C3 A:LA6704 3.2 53.4 0.5 O2A A:LA6704 3.2 51.9 0.5 O A:HOH807 3.4 58.5 1.0 O2A A:LA6704 3.6 51.1 0.5 PA A:LA6704 3.6 49.4 0.5 C5 A:LA6704 3.7 51.9 0.5 OD1 A:ASP488 3.8 47.7 1.0 F2 A:LA6704 3.9 52.1 0.5 PA A:LA6704 3.9 50.6 0.5 C6 A:LA6704 4.1 49.3 0.5 C9 A:LA6704 4.3 48.7 0.5 C9 A:LA6704 4.4 48.8 0.5 O3A A:LA6704 4.5 51.0 0.5 C6 A:LA6704 4.5 50.8 0.5 O A:HOH863 4.5 50.7 1.0 C4 A:LA6704 4.6 51.9 0.5 O3A A:LA6704 4.6 51.0 0.5 CG A:ASP488 4.7 41.7 1.0 O1A A:LA6704 4.8 51.7 0.5 OD2 A:ASP488 5.0 47.7 1.0

R.P.Kumar, B.R.Morehouse, J.O.Matos, K.Malik, H.Lin, I.J.Krauss, D.D.Oprian. Structural Characterization of Early Michaelis Complexes in the Reaction Catalyzed By (+)-Limonene Synthase From Citrus Sinensis Using Fluorinated Substrate Analogues. Biochemistry V. 56 1716 2017.
ISSN: ISSN 1520-4995
PubMed: 28272876
DOI: 10.1021/ACS.BIOCHEM.7B00144