Atomistry » Fluorine » PDB 3ccw-3d39 » 3cke
Atomistry »
  Fluorine »
    PDB 3ccw-3d39 »
      3cke »

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

Go back to Fluorine Binding Sites List in 3cke
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

Go back to Fluorine Binding Sites List in 3cke
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

Go back to Fluorine Binding Sites List in 3cke
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: Wed Jul 31 17:31:29 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy