Fluorine in PDB 6wkf: Crystal Structure of Pentalenene Synthase Mutant F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate

Enzymatic activity of Crystal Structure of Pentalenene Synthase Mutant F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Pentalenene Synthase Mutant F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate:
4.2.3.7;

Protein crystallography data

The structure of Crystal Structure of Pentalenene Synthase Mutant F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate, PDB code: 6wkf 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) 20.00 / 2.50
Space group P 63
Cell size a, b, c (Å), α, β, γ (°) 183.267, 183.267, 56.728, 90.00, 90.00, 120.00
R / Rfree (%) 20.8 / 23.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Pentalenene Synthase Mutant F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate (pdb code 6wkf). 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 F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate, PDB code: 6wkf:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 6wkf

Go back to Fluorine Binding Sites List in 6wkf
Fluorine binding site 1 out of 2 in the Crystal Structure of Pentalenene Synthase Mutant F76Y 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 F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:78.7
occ:1.00
F1 A:FDF401 0.0 78.7 1.0
C15 A:FDF401 1.4 82.2 1.0
C13 A:FDF401 2.4 79.0 1.0
F2 A:FDF401 2.6 81.4 1.0
OH A:TYR150 2.9 65.4 1.0
C14 A:FDF401 3.0 73.5 1.0
OH A:TYR146 3.0 68.6 1.0
O A:THR176 3.6 72.6 1.0
C12 A:FDF401 3.6 77.0 1.0
CE1 A:TYR146 3.8 57.2 1.0
CZ A:TYR146 3.9 58.7 1.0
O2A A:FDF401 3.9 99.0 1.0
CD1 A:TYR76 4.0 60.2 1.0
C11 A:FDF401 4.1 72.8 1.0
CZ A:TYR150 4.1 68.9 1.0
CB A:ASP80 4.4 50.8 1.0
CE1 A:TYR150 4.4 63.7 1.0
O A:TYR76 4.5 55.0 1.0
CE1 A:TYR76 4.5 65.7 1.0
O A:ILE177 4.5 62.3 1.0
OD1 A:ASP80 4.5 68.0 1.0
CG A:ASP80 4.6 64.6 1.0
CG A:TYR76 4.7 61.9 1.0
C A:ILE177 4.8 69.0 1.0
C A:THR176 4.8 73.0 1.0
CB A:TYR76 4.9 57.5 1.0

Fluorine binding site 2 out of 2 in 6wkf

Go back to Fluorine Binding Sites List in 6wkf
Fluorine binding site 2 out of 2 in the Crystal Structure of Pentalenene Synthase Mutant F76Y 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 F76Y Complexed with 12,13-Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:81.4
occ:1.00
F2 A:FDF401 0.0 81.4 1.0
C14 A:FDF401 1.4 73.5 1.0
C13 A:FDF401 2.4 79.0 1.0
F1 A:FDF401 2.6 78.7 1.0
C15 A:FDF401 2.9 82.2 1.0
O2A A:FDF401 2.9 99.0 1.0
CB A:ASP80 3.3 50.8 1.0
CG A:ASP80 3.4 64.6 1.0
OD2 A:ASP80 3.6 71.6 1.0
C12 A:FDF401 3.6 77.0 1.0
C1 A:FDF401 3.8 97.4 1.0
PA A:FDF401 3.8 0.3 1.0
O3A A:FDF401 3.9 0.4 1.0
OD1 A:ASP80 4.0 68.0 1.0
O A:TYR76 4.0 55.0 1.0
OH A:TYR150 4.1 65.4 1.0
O1 A:FDF401 4.2 0.1 1.0
CD2 A:PHE77 4.4 54.8 1.0
CE2 A:PHE77 4.5 60.1 1.0
C A:TYR76 4.6 55.5 1.0
CA A:ASP80 4.8 54.2 1.0
C2 A:FDF401 4.8 94.8 1.0
CA A:PHE77 4.8 58.8 1.0
C11 A:FDF401 4.9 72.8 1.0
CG A:PHE77 4.9 54.7 1.0
CZ A:PHE77 5.0 54.0 1.0

Reference:

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
Page generated: Sun Dec 13 13:31:58 2020

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