Fluorine in PDB 6onm: Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate

All present enzymatic activity of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate:
4.2.3.20;

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl Diphosphate, PDB code: 6onm was solved by R.Prem Kumar, B.R.Morehouse, Q.Yu, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.96 / 2.70
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	85.810, 85.810, 217.620, 90.00, 90.00, 90.00
R / Rfree (%)	20.6 / 24.1

The structure of Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl 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 8,9- Difluorolinalyl Diphosphate (pdb code 6onm). 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 8,9- Difluorolinalyl Diphosphate, PDB code: 6onm:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl 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 8,9- Difluorolinalyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:67.3 occ:1.00 F8 A:MWG704 0.0 67.3 1.0 C8 A:MWG704 1.4 64.2 1.0 F9 A:MWG704 2.3 74.9 1.0 C7 A:MWG704 2.4 71.7 1.0 C9 A:MWG704 2.8 76.7 1.0 OG1 A:THR446 3.5 55.2 1.0 C6 A:MWG704 3.7 74.3 1.0 CD1 A:ILE336 3.9 46.2 1.0 CG1 A:ILE336 3.9 45.2 1.0 CG1 A:ILE450 4.0 51.5 1.0 CD1 A:ILE450 4.2 43.1 1.0 CZ A:PHE484 4.3 57.5 1.0 CE3 A:TRP315 4.3 53.6 1.0 CD1 A:LEU557 4.4 49.5 1.0 CG2 A:ILE336 4.4 46.8 1.0 CE2 A:PHE484 4.5 62.8 1.0 CD2 A:TRP315 4.6 59.9 1.0 CZ3 A:TRP315 4.6 55.0 1.0 CB A:THR446 4.8 54.8 1.0 CB A:ILE336 4.8 51.8 1.0 O A:ILE445 4.9 57.0 1.0 C5 A:MWG704 4.9 83.4 1.0 CG A:TRP315 5.0 52.7 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of (+)-Limonene Synthase Complexed with 8,9- Difluorolinalyl 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 8,9- Difluorolinalyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F704 b:74.9 occ:1.00 F9 A:MWG704 0.0 74.9 1.0 C9 A:MWG704 1.4 76.7 1.0 F8 A:MWG704 2.3 67.3 1.0 C7 A:MWG704 2.4 71.7 1.0 C8 A:MWG704 2.8 64.2 1.0 OG1 A:THR446 3.6 55.2 1.0 C6 A:MWG704 3.6 74.3 1.0 CG2 A:ILE336 3.8 46.8 1.0 CG2 A:ILE339 3.8 53.5 1.0 CG1 A:ILE336 4.0 45.2 1.0 CG2 A:THR446 4.1 50.6 1.0 CD1 A:ILE339 4.2 46.9 1.0 C5 A:MWG704 4.3 83.4 1.0 CB A:ILE336 4.3 51.8 1.0 CB A:THR446 4.3 54.8 1.0 CB A:ILE339 4.3 51.2 1.0 CA A:ILE336 4.5 48.3 1.0 CD1 A:ILE336 4.7 46.2 1.0 CD1 A:ILE450 4.8 43.1 1.0 CG1 A:ILE339 4.9 54.3 1.0 O A:ILE336 4.9 53.4 1.0 C4 A:MWG704 4.9 85.0 1.0 CG1 A:ILE450 4.9 51.5 1.0 O A:ILE445 5.0 57.0 1.0

B.R.Morehouse, R.P.Kumar, J.O.Matos, Q.Yu, A.Bannister, K.Malik, J.S.Temme, I.J.Krauss, D.D.Oprian. Direct Evidence of An Enzyme-Generated Lpp Intermediate in (+)-Limonene Synthase Using A Fluorinated Gpp Substrate Analog. Acs Chem.Biol. V. 14 2035 2019.
ISSN: ESSN 1554-8937
PubMed: 31433159
DOI: 10.1021/ACSCHEMBIO.9B00514