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Fluorine in PDB 3bny: Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp)

Enzymatic activity of Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp)

All present enzymatic activity of Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp):
4.2.3.9;

Protein crystallography data

The structure of Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp), PDB code: 3bny was solved by E.Y.Shishova, D.W.Christianson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 22.33 / 1.89
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 61.654, 147.862, 83.954, 90.00, 97.84, 90.00
R / Rfree (%) 22.4 / 26.4

Other elements in 3bny:

The structure of Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp) also contains other interesting chemical elements:

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

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp) (pdb code 3bny). 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 Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp), PDB code: 3bny:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 3bny

Go back to Fluorine Binding Sites List in 3bny
Fluorine binding site 1 out of 4 in the Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp)


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 Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F400

b:38.4
occ:1.00
 F A:FPF400 0.0 38.4 1.0
C2 A:FPF400 1.2 39.7 1.0
C3 A:FPF400 2.1 34.5 1.0
C5 A:FPF400 2.5 32.8 1.0
C1 A:FPF400 2.5 45.2 1.0
ND2 A:ASN219 3.0 15.1 1.0
O1 A:FPF400 3.1 52.7 1.0
OD1 A:ASN219 3.3 21.1 1.0
NZ A:LYS181 3.4 26.9 1.0
CZ3 A:TRP308 3.4 20.5 1.0
C6 A:FPF400 3.5 31.6 1.0
CG A:ASN219 3.5 17.5 1.0
C4 A:FPF400 3.5 32.4 1.0
OD1 A:ASN305 3.6 15.6 1.0
CH2 A:TRP308 3.8 23.4 1.0
OH A:TYR67 3.9 20.9 1.0
CE3 A:TRP308 4.0 22.1 1.0
OH A:TYR315 4.2 22.7 1.0
C10 A:FPF400 4.6 31.5 1.0
P1 A:FPF400 4.6 57.3 1.0
CZ2 A:TRP308 4.7 21.6 1.0
C7 A:FPF400 4.7 32.3 1.0
CG A:ASN305 4.8 19.1 1.0
CE A:LYS181 4.8 27.7 1.0
CB A:ASN219 4.8 15.7 1.0
CD2 A:TRP308 4.8 21.3 1.0
CZ A:TYR67 4.9 21.1 1.0

Fluorine binding site 2 out of 4 in 3bny

Go back to Fluorine Binding Sites List in 3bny
Fluorine binding site 2 out of 4 in the Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp)


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 Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F401

b:52.4
occ:1.00
 F B:FPF401 0.0 52.4 1.0
C2 B:FPF401 1.3 53.8 1.0
C3 B:FPF401 2.2 51.1 1.0
C1 B:FPF401 2.4 57.4 1.0
C5 B:FPF401 2.7 49.5 1.0
ND2 B:ASN219 2.8 19.9 1.0
C6 B:FPF401 2.9 47.9 1.0
NZ B:LYS181 3.0 35.2 1.0
O1 B:FPF401 3.5 63.3 1.0
C4 B:FPF401 3.6 50.8 1.0
CG B:ASN219 3.6 22.3 1.0
ND2 B:ASN305 3.8 19.2 1.0
OD1 B:ASN219 3.8 27.3 1.0
C7 B:FPF401 4.0 47.5 1.0
CZ3 B:TRP308 4.1 24.4 1.0
C10 B:FPF401 4.1 45.9 1.0
O1A B:FPF401 4.2 64.9 1.0
CE B:LYS181 4.3 32.6 1.0
OH B:TYR67 4.3 22.0 1.0
CH2 B:TRP308 4.4 24.5 1.0
C8 B:FPF401 4.5 47.3 1.0
P1 B:FPF401 4.5 65.8 1.0
O B:HOH1281 4.5 23.0 1.0
OH B:TYR315 4.6 26.9 1.0
O B:HOH1379 4.6 36.7 1.0
CE3 B:TRP308 4.7 25.2 1.0
CB B:ASN219 4.9 20.5 1.0

Fluorine binding site 3 out of 4 in 3bny

Go back to Fluorine Binding Sites List in 3bny
Fluorine binding site 3 out of 4 in the Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp)


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 Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:52.0
occ:1.00
 F C:FPF402 0.0 52.0 1.0
C2 C:FPF402 1.3 51.8 1.0
C3 C:FPF402 2.2 49.6 1.0
C1 C:FPF402 2.4 54.5 1.0
C5 C:FPF402 2.7 48.2 1.0
ND2 C:ASN219 2.8 16.4 1.0
O1 C:FPF402 2.9 59.0 1.0
CZ3 C:TRP308 3.1 20.9 1.0
CG C:ASN219 3.2 17.3 1.0
OD1 C:ASN219 3.2 20.6 1.0
C6 C:FPF402 3.3 45.5 1.0
C4 C:FPF402 3.6 48.2 1.0
CH2 C:TRP308 3.7 21.7 1.0
ND2 C:ASN305 3.7 15.3 1.0
OH C:TYR315 3.8 22.6 1.0
CE3 C:TRP308 3.9 20.5 1.0
OH C:TYR67 4.2 20.8 1.0
P1 C:FPF402 4.2 62.1 1.0
O3A C:FPF402 4.3 62.1 1.0
O3B C:FPF402 4.3 63.5 1.0
CB C:ASN219 4.4 17.0 1.0
C7 C:FPF402 4.5 43.2 1.0
CE C:LYS181 4.7 31.3 1.0
O C:HOH1355 4.7 30.0 1.0
CZ2 C:TRP308 4.8 22.4 1.0
NZ C:LYS181 4.8 36.7 1.0
C10 C:FPF402 4.8 43.4 1.0
P2 C:FPF402 4.9 65.0 1.0
O1A C:FPF402 4.9 62.6 1.0
CG C:ASN305 4.9 19.5 1.0
CZ C:TYR315 5.0 23.1 1.0
CD2 C:TRP308 5.0 20.4 1.0

Fluorine binding site 4 out of 4 in 3bny

Go back to Fluorine Binding Sites List in 3bny
Fluorine binding site 4 out of 4 in the Crystal Structure of Aristolochene Synthase Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp)


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 Complexed with 2-Fluorofarnesyl Diphosphate (2F-Fpp) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:41.3
occ:1.00
 F D:FPF403 0.0 41.3 1.0
C2 D:FPF403 1.3 38.5 1.0
C1 D:FPF403 2.2 37.0 1.0
C3 D:FPF403 2.4 39.5 1.0
C5 D:FPF403 2.8 41.0 1.0
C10 D:FPF403 2.9 42.0 1.0
O D:HOH1287 3.0 29.3 1.0
NZ D:LYS181 3.2 24.0 1.0
C6 D:FPF403 3.2 42.5 1.0
CE D:LYS181 3.3 25.9 1.0
O1 D:FPF403 3.4 35.2 1.0
C4 D:FPF403 3.5 36.8 1.0
C8 D:FPF403 3.7 43.7 1.0
O D:HOH1356 3.7 32.6 1.0
C7 D:FPF403 3.9 42.6 1.0
CD D:LYS181 4.0 27.3 1.0
O1A D:FPF403 4.6 31.9 1.0
P1 D:FPF403 4.6 31.3 1.0
C9 D:FPF403 4.8 44.2 1.0
ND2 D:ASN219 4.9 20.7 1.0
CG D:ASN219 4.9 17.2 1.0
C12 D:FPF403 4.9 46.2 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 17:17:40 2024

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