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Fluorine in PDB 9c7j: Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate

Enzymatic activity of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate:
4.2.1.138; 4.2.3.89;

Protein crystallography data

The structure of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate, PDB code: 9c7j was solved by R.Prem Kumar, B.Y.Black, D.D.Oprian, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.99 / 2.65
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 68.648, 89.606, 114.814, 90, 90.71, 90
R / Rfree (%) 20.4 / 24.9

Other elements in 9c7j:

The structure of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate also contains other interesting chemical elements:

Magnesium (Mg) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate (pdb code 9c7j). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate, PDB code: 9c7j:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 9c7j

Go back to Fluorine Binding Sites List in 9c7j
Fluorine binding site 1 out of 4 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl 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 Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F401

b:57.0
occ:1.00
 F A:FPF401 0.0 57.0 1.0
C2 A:FPF401 1.4 52.1 1.0
C3 A:FPF401 2.3 42.2 1.0
C1 A:FPF401 2.5 56.5 1.0
C5 A:FPF401 2.8 39.5 1.0
CB A:ASP83 3.1 43.2 1.0
C6 A:FPF401 3.2 41.4 1.0
O1 A:FPF401 3.3 69.8 1.0
OD2 A:ASP83 3.3 50.1 1.0
CG A:ASP83 3.5 43.6 1.0
OH A:TYR152 3.6 37.7 1.0
O A:ALA79 3.7 31.9 1.0
C4 A:FPF401 3.7 48.8 1.0
CD1 A:PHE80 4.1 36.7 1.0
C A:ALA79 4.2 32.4 1.0
CE1 A:PHE80 4.4 31.1 1.0
CA A:PHE80 4.4 29.2 1.0
CA A:ASP83 4.5 45.4 1.0
OD1 A:ASP83 4.6 51.8 1.0
N A:PHE80 4.6 31.2 1.0
C7 A:FPF401 4.6 44.7 1.0
NE1 A:TRP148 4.6 31.6 1.0
CZ2 A:TRP148 4.7 28.4 1.0
N A:ASP83 4.7 39.9 1.0
MG A:MG403 4.8 53.8 1.0
CB A:ALA79 4.8 23.4 1.0
P1 A:FPF401 4.9 82.1 1.0

Fluorine binding site 2 out of 4 in 9c7j

Go back to Fluorine Binding Sites List in 9c7j
Fluorine binding site 2 out of 4 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl 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 Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:61.0
occ:0.77
 F B:FPF401 0.0 61.0 0.8
C2 B:FPF401 1.4 60.6 0.8
C3 B:FPF401 2.3 57.6 0.8
C1 B:FPF401 2.5 67.2 0.8
C5 B:FPF401 2.7 46.6 0.8
OD1 B:ASP83 2.8 55.4 1.0
CG B:ASP83 3.0 60.6 1.0
CB B:ASP83 3.1 46.9 1.0
C6 B:FPF401 3.2 45.8 0.8
OH B:TYR152 3.3 37.5 1.0
O1 B:FPF401 3.4 68.0 0.8
C4 B:FPF401 3.7 60.0 0.8
OD2 B:ASP83 3.8 70.4 1.0
O B:ALA79 4.3 33.0 1.0
CA B:ASP83 4.3 46.0 1.0
NE1 B:TRP148 4.5 36.7 1.0
CD1 B:PHE80 4.6 42.9 1.0
C7 B:FPF401 4.6 45.6 0.8
CZ B:TYR152 4.7 40.3 1.0
CE1 B:PHE80 4.8 43.0 1.0
P1 B:FPF401 4.8 74.5 0.8
O2A B:FPF401 4.8 70.8 0.8
N B:ASP83 4.8 37.3 1.0
C B:ALA79 5.0 33.2 1.0

Fluorine binding site 3 out of 4 in 9c7j

Go back to Fluorine Binding Sites List in 9c7j
Fluorine binding site 3 out of 4 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F401

b:60.0
occ:0.77
 F C:FPF401 0.0 60.0 0.8
C2 C:FPF401 1.4 56.8 0.8
C3 C:FPF401 2.3 51.3 0.8
C1 C:FPF401 2.5 60.9 0.8
C5 C:FPF401 2.8 46.8 0.8
O1 C:FPF401 2.8 62.9 0.8
CE1 C:PHE80 3.0 46.8 1.0
CZ C:PHE80 3.5 42.0 1.0
C4 C:FPF401 3.7 48.1 0.8
O2A C:FPF401 3.9 74.4 0.8
C6 C:FPF401 3.9 44.6 0.8
P1 C:FPF401 4.0 65.7 0.8
CD1 C:PHE80 4.0 46.5 1.0
CB C:ALA179 4.6 45.5 1.0
CE2 C:PHE80 4.7 42.6 1.0
O1A C:FPF401 4.7 75.9 0.8
C7 C:FPF401 4.9 45.8 0.8

Fluorine binding site 4 out of 4 in 9c7j

Go back to Fluorine Binding Sites List in 9c7j
Fluorine binding site 4 out of 4 in the Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Caryolan-1-Ol Synthase Complexed with 2- Fluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F401

b:64.6
occ:1.00
 F D:FPF401 0.0 64.6 1.0
C2 D:FPF401 1.4 61.2 1.0
C3 D:FPF401 2.3 55.8 1.0
C1 D:FPF401 2.5 63.8 1.0
O2A D:FPF401 2.6 73.9 1.0
C5 D:FPF401 2.7 52.7 1.0
O1 D:FPF401 2.7 73.3 1.0
P1 D:FPF401 3.0 80.6 1.0
O1A D:FPF401 3.4 63.8 1.0
C4 D:FPF401 3.7 46.0 1.0
C6 D:FPF401 4.0 43.8 1.0
C7 D:FPF401 4.3 46.2 1.0
ND2 D:ASN220 4.4 53.6 1.0
CH2 D:TRP56 4.4 32.5 1.0
O D:SER177 4.4 44.5 1.0
N D:ALA179 4.5 53.5 1.0
CZ3 D:TRP56 4.5 33.9 1.0
O3A D:FPF401 4.6 76.3 1.0
CB D:ALA179 4.6 48.1 1.0
CE1 D:PHE80 4.6 37.1 1.0
CA D:VAL178 4.9 50.3 1.0
O3B D:FPF401 5.0 81.7 1.0

Reference:

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
Page generated: Wed Jul 16 10:39:33 2025

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