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Fluorine in PDB 3cke: Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate

Enzymatic activity of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate

All present enzymatic activity of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate:
4.2.3.9;

Protein crystallography data

The structure of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate, PDB code: 3cke was solved by E.Y.Shishova, F.Yu, D.J.Miller, J.A.Faraldos, Y.Zhao, R.M.Coates, R.K.Allemann, D.E.Cane, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 56.30 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.534, 146.842, 84.110, 90.00, 97.87, 90.00
R / Rfree (%) 24.5 / 29

Other elements in 3cke:

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

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate (pdb code 3cke). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate, PDB code: 3cke:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 3cke

Go back to Fluorine Binding Sites List in 3cke
Fluorine binding site 1 out of 6 in the Crystal Structure of Aristolochene Synthase in Complex 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 Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:78.5
occ:1.00
 F1 A:FDF400 0.0 78.5 1.0
C15 A:FDF400 1.3 76.7 1.0
C13 A:FDF400 2.5 75.8 1.0
C2 A:FDF400 3.0 72.3 1.0
C14 A:FDF400 3.1 78.0 1.0
O1 A:FDF400 3.2 79.8 1.0
O1B A:FDF400 3.2 68.2 1.0
C1 A:FDF400 3.3 75.6 1.0
F2 A:FDF400 3.4 81.3 1.0
C12 A:FDF400 3.5 72.5 1.0
O3B A:FDF400 3.5 75.8 1.0
PB A:FDF400 3.9 74.5 1.0
C11 A:FDF400 3.9 67.7 1.0
NH2 A:ARG314 4.0 36.7 1.0
C3 A:FDF400 4.1 69.5 1.0
CZ A:ARG314 4.2 42.5 1.0
PA A:FDF400 4.2 79.1 1.0
NE A:ARG314 4.3 38.1 1.0
O3A A:FDF400 4.4 74.8 1.0
C8 A:FDF400 4.6 63.9 1.0
C7 A:FDF400 4.6 62.8 1.0
CE2 A:PHE87 4.6 47.6 1.0
C5 A:FDF400 4.6 65.9 1.0
C9 A:FDF400 4.8 64.8 1.0
NH1 A:ARG314 4.8 43.8 1.0
O1A A:FDF400 4.8 84.8 1.0
CZ A:PHE153 4.9 37.2 1.0
C10 A:FDF400 5.0 65.0 1.0
CZ A:PHE87 5.0 47.5 1.0

Fluorine binding site 2 out of 6 in 3cke

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Fluorine binding site 2 out of 6 in the Crystal Structure of Aristolochene Synthase in Complex 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 Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:81.3
occ:1.00
 F2 A:FDF400 0.0 81.3 1.0
C14 A:FDF400 1.3 78.0 1.0
C13 A:FDF400 2.3 75.8 1.0
C15 A:FDF400 2.8 76.7 1.0
CB A:ASP90 3.0 53.7 1.0
CG A:ASP90 3.1 58.7 1.0
OD2 A:ASP90 3.2 57.5 1.0
C12 A:FDF400 3.4 72.5 1.0
F1 A:FDF400 3.4 78.5 1.0
OD1 A:ASP90 3.7 59.1 1.0
CA A:PHE87 3.8 37.3 1.0
CD2 A:PHE87 3.9 44.3 1.0
O A:LEU86 3.9 41.7 1.0
NH2 A:ARG314 4.0 36.7 1.0
NE2 A:GLN157 4.3 63.8 1.0
O A:PHE87 4.3 39.8 1.0
N A:PHE87 4.3 35.0 1.0
C A:LEU86 4.4 41.4 1.0
CG A:PHE87 4.4 41.5 1.0
CE2 A:PHE87 4.4 47.6 1.0
NH1 A:ARG314 4.4 43.8 1.0
CA A:ASP90 4.5 50.9 1.0
O3B A:FDF400 4.5 75.8 1.0
CZ A:ARG314 4.5 42.5 1.0
C A:PHE87 4.5 40.4 1.0
CB A:PHE87 4.6 34.3 1.0
C11 A:FDF400 4.7 67.7 1.0
CZ A:PHE153 5.0 37.2 1.0
N A:ASP90 5.0 45.3 1.0

Fluorine binding site 3 out of 6 in 3cke

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Fluorine binding site 3 out of 6 in the Crystal Structure of Aristolochene Synthase in Complex 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 3 of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:58.2
occ:1.00
 F1 B:FDF401 0.0 58.2 1.0
C15 B:FDF401 1.3 60.3 1.0
C13 B:FDF401 2.5 61.4 1.0
C11 B:FDF401 2.6 66.3 1.0
C12 B:FDF401 2.9 62.2 1.0
OH B:TYR67 3.2 34.0 1.0
OD1 B:ASN305 3.5 32.5 1.0
CE2 B:TYR67 3.7 29.1 1.0
CZ B:TYR67 3.7 31.2 1.0
C14 B:FDF401 3.8 58.6 1.0
C9 B:FDF401 3.8 72.8 1.0
CD1 B:LEU184 3.8 23.7 1.0
C10 B:FDF401 4.0 66.8 1.0
F2 B:FDF401 4.0 50.7 1.0
OD1 B:ASN219 4.1 30.8 1.0
C8 B:FDF401 4.4 80.3 1.0
CE B:LYS181 4.5 33.4 1.0
CG B:ASN305 4.6 30.9 1.0
CZ3 B:TRP308 4.7 31.2 1.0
CD2 B:TYR67 4.8 31.5 1.0
CE1 B:TYR67 4.8 30.8 1.0
CD B:LYS181 4.8 27.4 1.0
CE3 B:TRP308 4.9 36.7 1.0
CG B:ASN219 4.9 30.1 1.0
ND2 B:ASN219 4.9 32.5 1.0
CG B:LEU184 5.0 30.7 1.0

Fluorine binding site 4 out of 6 in 3cke

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Fluorine binding site 4 out of 6 in the Crystal Structure of Aristolochene Synthase in Complex 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 4 of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:50.7
occ:1.00
 F2 B:FDF401 0.0 50.7 1.0
C14 B:FDF401 1.4 58.6 1.0
O2A B:FDF401 2.0 54.1 1.0
C13 B:FDF401 2.3 61.4 1.0
C15 B:FDF401 2.8 60.3 1.0
PA B:FDF401 3.3 66.3 1.0
O1B B:FDF401 3.4 55.8 1.0
O1A B:FDF401 3.5 60.1 1.0
C12 B:FDF401 3.5 62.2 1.0
OH B:TYR315 3.8 43.7 1.0
C1 B:FDF401 3.9 63.0 1.0
F1 B:FDF401 4.0 58.2 1.0
O B:HOH1346 4.0 48.0 1.0
O2B B:FDF401 4.1 56.8 1.0
CH2 B:TRP308 4.1 33.4 1.0
OD1 B:ASN219 4.2 30.8 1.0
PB B:FDF401 4.2 70.0 1.0
O1 B:FDF401 4.2 60.3 1.0
CZ3 B:TRP308 4.3 31.2 1.0
O B:HOH1337 4.4 35.5 1.0
O3A B:FDF401 4.5 58.3 1.0
C2 B:FDF401 4.6 57.1 1.0
C11 B:FDF401 4.8 66.3 1.0
CG B:ASN219 4.8 30.1 1.0
C10 B:FDF401 4.8 66.8 1.0
CZ B:TYR315 4.9 38.0 1.0

Fluorine binding site 5 out of 6 in 3cke

Go back to Fluorine Binding Sites List in 3cke
Fluorine binding site 5 out of 6 in the Crystal Structure of Aristolochene Synthase in Complex 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 5 of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:74.6
occ:1.00
 F1 C:FDF402 0.0 74.6 1.0
C15 C:FDF402 1.3 63.3 1.0
C13 C:FDF402 2.2 60.8 1.0
C14 C:FDF402 2.8 63.4 1.0
NH2 C:ARG314 2.9 43.8 1.0
C12 C:FDF402 3.2 55.3 1.0
O1 C:FDF402 3.3 78.0 1.0
CZ C:ARG314 3.5 44.2 1.0
F2 C:FDF402 3.6 64.0 1.0
C11 C:FDF402 3.7 53.6 1.0
CE2 C:PHE87 3.8 62.9 1.0
OD2 C:ASP90 3.8 51.6 1.0
NE C:ARG314 3.9 45.6 1.0
O1A C:FDF402 4.0 66.0 1.0
C1 C:FDF402 4.0 73.5 1.0
CD2 C:PHE87 4.0 63.6 1.0
C2 C:FDF402 4.0 67.9 1.0
CG C:ASP90 4.1 58.1 1.0
CZ C:PHE87 4.1 62.5 1.0
PA C:FDF402 4.3 70.6 1.0
NH1 C:ARG314 4.3 44.6 1.0
CG C:PHE87 4.4 58.3 1.0
CB C:ASP90 4.5 58.5 1.0
CE1 C:PHE87 4.5 65.0 1.0
O1B C:FDF402 4.5 73.9 1.0
OD1 C:ASP90 4.5 56.9 1.0
CD1 C:PHE87 4.6 59.1 1.0
CA C:PHE87 4.8 50.5 1.0

Fluorine binding site 6 out of 6 in 3cke

Go back to Fluorine Binding Sites List in 3cke
Fluorine binding site 6 out of 6 in the Crystal Structure of Aristolochene Synthase in Complex 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 6 of Crystal Structure of Aristolochene Synthase in Complex with 12,13- Difluorofarnesyl Diphosphate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:64.0
occ:1.00
 F2 C:FDF402 0.0 64.0 1.0
C14 C:FDF402 1.3 63.4 1.0
C13 C:FDF402 2.1 60.8 1.0
C12 C:FDF402 2.3 55.3 1.0
CZ C:PHE153 2.6 41.2 1.0
C15 C:FDF402 3.3 63.3 1.0
CE2 C:PHE153 3.3 31.8 1.0
F1 C:FDF402 3.6 74.6 1.0
CE1 C:PHE153 3.7 40.9 1.0
C11 C:FDF402 3.8 53.6 1.0
NE2 C:GLN157 3.8 77.0 1.0
OD1 C:ASP90 4.2 56.9 1.0
O1 C:FDF402 4.3 78.0 1.0
C9 C:FDF402 4.4 52.8 1.0
CG C:GLN157 4.4 74.0 1.0
CD C:GLN157 4.4 75.8 1.0
CG C:ASP90 4.6 58.1 1.0
CD2 C:PHE153 4.7 37.1 1.0
CB C:ASP90 4.8 58.5 1.0
O2A C:FDF402 4.8 70.4 1.0
CD1 C:PHE153 4.9 42.0 1.0
PA C:FDF402 5.0 70.6 1.0

Reference:

E.Y.Shishova, F.Yu, D.J.Miller, J.A.Faraldos, Y.Zhao, R.M.Coates, R.K.Allemann, D.E.Cane, D.W.Christianson. X-Ray Crystallographic Studies of Substrate Binding to Aristolochene Synthase Suggest A Metal Ion Binding Sequence For Catalysis. J.Biol.Chem. V. 283 15431 2008.
ISSN: ISSN 0021-9258
PubMed: 18385128
DOI: 10.1074/JBC.M800659200
Page generated: Sun Dec 13 11:43:58 2020

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