Fluorine in PDB 9c7m: Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate:
4.2.3.7;

The structure of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate, PDB code: 9c7m was solved by R.Prem Kumar, W.H.Ellenburg, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.80 / 2.65
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	180.53, 180.53, 55.861, 90, 90, 120
R / Rfree (%)	19.8 / 23

The structure of Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate also contains other interesting chemical elements:

Magnesium

(Mg)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of Pentalenene Synthase Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate (pdb code 9c7m). 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 Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate, PDB code: 9c7m:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in the Crystal Structure of Pentalenene Synthase Variant F76A 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 Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:108.8 occ:1.00 F1 A:FDF401 0.0 108.8 1.0 C15 A:FDF401 1.4 98.0 1.0 C13 A:FDF401 2.4 92.6 1.0 F2 A:FDF401 2.5 104.6 1.0 C14 A:FDF401 2.9 98.6 1.0 CD1 A:ILE177 3.3 82.8 1.0 CG1 A:ILE177 3.5 81.1 1.0 C12 A:FDF401 3.6 87.8 1.0 OD1 A:ASN215 3.6 83.2 1.0 O A:ASN215 3.7 78.5 1.0 CB A:ASN215 3.7 76.9 1.0 C A:ASN215 4.0 78.5 1.0 CE1 A:HIS309 4.0 99.7 1.0 CB A:ASN219 4.1 88.2 1.0 CG A:ASN215 4.2 79.4 1.0 OG A:SER305 4.3 96.8 1.0 CA A:ASN215 4.3 78.7 1.0 ND2 A:ASN219 4.4 92.5 1.0 NE2 A:HIS309 4.5 97.1 1.0 O A:ILE177 4.5 82.8 1.0 N A:LEU216 4.6 72.5 1.0 CG A:ASN219 4.6 91.7 1.0 CG2 A:VAL179 4.8 68.7 1.0 C11 A:FDF401 4.9 87.3 1.0 CA A:LEU216 5.0 80.9 1.0

Fluorine binding site 2 out of 2 in the Crystal Structure of Pentalenene Synthase Variant F76A 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 Variant F76A Complexed with 12,13-Difluorofarnesyl Diphosphate within 5.0Å range: probe atom residue distance (Å) B Occ A:F401 b:104.6 occ:1.00 F2 A:FDF401 0.0 104.6 1.0 C14 A:FDF401 1.4 98.6 1.0 C13 A:FDF401 2.4 92.6 1.0 F1 A:FDF401 2.5 108.8 1.0 C15 A:FDF401 2.9 98.0 1.0 ND2 A:ASN219 3.2 92.5 1.0 C12 A:FDF401 3.7 87.8 1.0 NE2 A:HIS309 4.0 97.1 1.0 CE1 A:HIS309 4.0 99.7 1.0 CG A:ASN219 4.0 91.7 1.0 C2 A:FDF401 4.1 99.4 1.0 C1 A:FDF401 4.1 104.3 1.0 C11 A:FDF401 4.2 87.3 1.0 OH A:TYR315 4.2 97.5 1.0 O1 A:FDF401 4.2 103.5 1.0 CB A:ASN219 4.3 88.2 1.0 CD1 A:ILE177 4.4 82.8 1.0 CZ A:PHE77 4.4 76.4 1.0 O1B A:FDF401 4.7 113.5 1.0 C3 A:FDF401 4.7 93.4 1.0 CE1 A:PHE77 4.8 81.1 1.0 CZ3 A:TRP308 4.8 86.8 1.0 OD1 A:ASN219 4.9 94.6 1.0 O A:ILE177 5.0 82.8 1.0

R.P.Kumar, J.O.Matos, B.Y.Black, W.H.Ellenburg, J.Chen, M.Patterson, J.A.Gehtman, D.L.Theobald, I.J.Krauss, D.D.Oprian. Crystal Structure of Caryolan-1-Ol Synthase, A Sesquiterpene Synthase Catalyzing An Initial Anti-Markovnikov Cyclization Reaction. Biochemistry 2024.
ISSN: ISSN 0006-2960
PubMed: 39400323
DOI: 10.1021/ACS.BIOCHEM.4C00547