Fluorine in PDB 6wkh: Crystal Structure of Pentalenene Synthase Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate:
4.2.3.7;

The structure of Crystal Structure of Pentalenene Synthase Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate, PDB code: 6wkh 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)	19.89 / 2.55
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	185.019, 185.019, 56.930, 90.00, 90.00, 120.00
R / Rfree (%)	22.5 / 25.6

The binding sites of Fluorine atom in the Crystal Structure of Pentalenene Synthase Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate (pdb code 6wkh). 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 Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate, PDB code: 6wkh:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Pentalenene Synthase Mutant F76W 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 Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:0.9 occ:1.00 F1 A:FDF401 0.0 0.9 1.0 C15 A:FDF401 1.4 89.0 1.0 F2 A:FDF401 2.4 82.7 1.0 C13 A:FDF401 2.4 88.9 1.0 C14 A:FDF401 2.9 78.0 1.0 O2A A:FDF401 3.3 0.1 1.0 C1 A:FDF401 3.3 0.2 1.0 NE1 A:TRP76 3.4 69.2 1.0 C12 A:FDF401 3.6 86.4 1.0 O1 A:FDF401 3.8 0.6 1.0 CD1 A:TRP76 3.8 68.7 1.0 OH A:TYR146 3.9 70.5 1.0 O A:THR176 3.9 75.3 1.0 C2 A:FDF401 4.1 0.2 1.0 CE2 A:TRP76 4.1 57.2 1.0 PA A:FDF401 4.1 0.3 1.0 C11 A:FDF401 4.2 73.7 1.0 O A:ILE177 4.3 73.9 1.0 CG A:TRP76 4.6 60.0 1.0 CZ2 A:TRP76 4.6 69.5 1.0 CE1 A:TYR146 4.6 58.7 1.0 CZ A:TYR146 4.7 57.6 1.0 O1A A:FDF401 4.7 1.0 1.0 CD2 A:TRP76 4.7 61.3 1.0 C A:ILE177 4.8 72.1 1.0 CG A:ASP80 5.0 87.0 1.0 OD1 A:ASP80 5.0 77.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Pentalenene Synthase Mutant F76W 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 Mutant F76W Complexed with 12,13-Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:82.7 occ:1.00 F2 A:FDF401 0.0 82.7 1.0 C14 A:FDF401 1.4 78.0 1.0 F1 A:FDF401 2.4 0.9 1.0 C13 A:FDF401 2.4 88.9 1.0 C15 A:FDF401 2.9 89.0 1.0 O2A A:FDF401 2.9 0.1 1.0 CB A:ASP80 3.5 64.8 1.0 C1 A:FDF401 3.7 0.2 1.0 C12 A:FDF401 3.7 86.4 1.0 CD1 A:TRP76 3.8 68.7 1.0 CG A:ASP80 3.8 87.0 1.0 OD2 A:ASP80 4.0 92.0 1.0 O A:TRP76 4.0 53.4 1.0 O1B A:FDF401 4.2 0.2 1.0 CD1 A:PHE77 4.2 47.2 1.0 PA A:FDF401 4.2 0.3 1.0 CE1 A:PHE77 4.2 55.6 1.0 NE1 A:TRP76 4.3 69.2 1.0 O1 A:FDF401 4.4 0.6 1.0 OD1 A:ASP80 4.4 77.9 1.0 C A:TRP76 4.5 51.1 1.0 CG A:TRP76 4.5 60.0 1.0 CG A:PHE77 4.6 52.1 1.0 CA A:PHE77 4.6 56.5 1.0 CZ A:PHE77 4.7 52.1 1.0 N A:PHE77 4.8 56.3 1.0 C2 A:FDF401 4.8 0.2 1.0 CB A:TRP76 4.9 51.9 1.0 C11 A:FDF401 4.9 73.7 1.0 O2B A:FDF401 4.9 0.7 1.0 CA A:ASP80 5.0 60.5 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