Fluorine in PDB 6wkd: Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate:
4.2.3.7;

The structure of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate, PDB code: 6wkd was solved by R.Prem Kumar, J.O.Matos, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.97 / 2.20
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	182.467, 182.467, 56.212, 90.00, 90.00, 120.00
R / Rfree (%)	20.1 / 22

The structure of Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Fluorine atom in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate (pdb code 6wkd). 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 Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate, PDB code: 6wkd:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl 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 Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:48.3 occ:1.00 F1 A:FDF401 0.0 48.3 1.0 C15 A:FDF401 1.4 47.7 1.0 C13 A:FDF401 2.4 51.8 1.0 OH A:TYR146 2.6 38.7 1.0 C14 A:FDF401 2.9 50.2 1.0 OH A:TYR150 2.9 44.8 1.0 O A:HOH608 3.2 60.3 1.0 F2 A:FDF401 3.4 56.2 1.0 C12 A:FDF401 3.6 46.0 1.0 CZ A:TYR146 3.6 35.5 1.0 CE1 A:TYR146 3.6 36.6 1.0 CD1 A:PHE76 3.8 33.6 1.0 O A:THR176 3.9 41.9 1.0 O A:PHE76 4.1 36.5 1.0 CZ A:TYR150 4.1 49.4 1.0 C11 A:FDF401 4.1 43.5 1.0 CB A:ASP80 4.2 36.7 1.0 CE1 A:PHE76 4.3 35.3 1.0 OD1 A:ASP80 4.4 48.0 1.0 CG A:ASP80 4.5 46.7 1.0 CE1 A:TYR150 4.5 46.7 1.0 CG A:PHE76 4.5 33.6 1.0 CB A:PHE76 4.7 35.1 1.0 C A:PHE76 4.8 38.7 1.0 CE2 A:TYR146 4.9 36.4 1.0 O A:ILE177 4.9 43.0 1.0 CD1 A:TYR146 5.0 38.5 1.0 CA A:PHE76 5.0 28.4 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl 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 Pentalenene Synthase Complexed with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:56.2 occ:1.00 F2 A:FDF401 0.0 56.2 1.0 C14 A:FDF401 1.4 50.2 1.0 C13 A:FDF401 2.4 51.8 1.0 C12 A:FDF401 3.1 46.0 1.0 CD2 A:PHE77 3.2 39.8 1.0 O A:PHE76 3.3 36.5 1.0 F1 A:FDF401 3.4 48.3 1.0 CG A:PHE77 3.4 40.2 1.0 CE2 A:PHE77 3.5 43.8 1.0 C15 A:FDF401 3.5 47.7 1.0 O A:HOH504 3.5 60.7 1.0 C A:PHE76 3.6 38.7 1.0 CA A:PHE77 3.6 39.5 1.0 CB A:ASP80 3.7 36.7 1.0 N A:PHE77 3.7 37.2 1.0 CD1 A:PHE77 3.8 35.8 1.0 CZ A:PHE77 3.9 37.4 1.0 CE1 A:PHE77 4.0 36.1 1.0 CB A:PHE77 4.1 33.8 1.0 CB A:PHE76 4.1 35.1 1.0 CG A:ASP80 4.2 46.7 1.0 OD2 A:ASP80 4.3 54.4 1.0 CA A:PHE76 4.4 28.4 1.0 C1 A:FDF401 4.4 61.4 1.0 C11 A:FDF401 4.5 43.5 1.0 O A:HOH526 4.6 53.8 1.0 C A:PHE77 4.8 32.1 1.0 CG A:PHE76 4.8 33.6 1.0 O2A A:FDF401 5.0 70.5 1.0

J.O.Matos, R.P.Kumar, A.C.Ma, M.Patterson, I.J.Krauss, D.D.Oprian. Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase. Biochemistry V. 59 3271 2020.
ISSN: ISSN 0006-2960
PubMed: 32786410
DOI: 10.1021/ACS.BIOCHEM.0C00518