Fluorine in PDB 5yas: Hydroxynitrile Lyase Complexed with Hexafluoroacetone

Enzymatic activity of Hydroxynitrile Lyase Complexed with Hexafluoroacetone

All present enzymatic activity of Hydroxynitrile Lyase Complexed with Hexafluoroacetone:
4.1.2.39;

Protein crystallography data

The structure of Hydroxynitrile Lyase Complexed with Hexafluoroacetone, PDB code: 5yas was solved by J.Zuegg, U.G.Wagner, M.Gugganig, C.Kratky, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 16.00 / 2.20
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 47.461, 106.441, 128.154, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone (pdb code 5yas). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone, PDB code: 5yas:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5yas

Go back to Fluorine Binding Sites List in 5yas
Fluorine binding site 1 out of 6 in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Hydroxynitrile Lyase Complexed with Hexafluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:32.7
occ:1.00
 F1 A:FAC300 0.0 32.7 1.0
C1 A:FAC300 1.4 30.9 1.0
F3 A:FAC300 2.2 30.6 1.0
F2 A:FAC300 2.3 30.6 1.0
C A:FAC300 2.4 32.5 1.0
F4 A:FAC300 2.7 33.4 1.0
C2 A:FAC300 2.8 33.9 1.0
O2 A:FAC300 3.0 29.9 1.0
F6 A:FAC300 3.3 35.4 1.0
CH2 A:TRP128 3.6 7.0 1.0
O1 A:FAC300 3.6 31.0 1.0
CD1 A:ILE209 3.8 13.3 1.0
CZ3 A:TRP128 3.8 6.7 1.0
CE1 A:PHE210 3.9 2.7 1.0
OG A:SER80 4.1 7.4 1.0
F5 A:FAC300 4.1 39.1 1.0
CG2 A:ILE209 4.3 4.7 1.0
CZ2 A:TRP128 4.5 11.6 1.0
CZ A:PHE210 4.7 2.9 1.0
O A:HOH500 4.8 5.9 1.0
CD1 A:PHE210 4.8 2.3 1.0
CB A:ILE209 4.8 6.4 1.0
CE3 A:TRP128 4.9 4.4 1.0

Fluorine binding site 2 out of 6 in 5yas

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Fluorine binding site 2 out of 6 in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Hydroxynitrile Lyase Complexed with Hexafluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:30.6
occ:1.00
 F2 A:FAC300 0.0 30.6 1.0
C1 A:FAC300 1.4 30.9 1.0
F3 A:FAC300 2.2 30.6 1.0
F1 A:FAC300 2.3 32.7 1.0
C A:FAC300 2.3 32.5 1.0
O1 A:FAC300 2.6 31.0 1.0
F6 A:FAC300 2.8 35.4 1.0
C2 A:FAC300 3.0 33.9 1.0
CD2 A:LEU157 3.4 3.2 1.0
CD1 A:LEU157 3.6 3.3 1.0
O2 A:FAC300 3.6 29.9 1.0
CD2 A:LEU148 3.6 3.4 1.0
CD1 A:LEU148 3.7 4.0 1.0
F4 A:FAC300 3.8 33.4 1.0
CG A:LEU157 3.8 4.4 1.0
CZ3 A:TRP128 4.0 6.7 1.0
F5 A:FAC300 4.1 39.1 1.0
CG A:LEU148 4.3 5.7 1.0
CD1 A:ILE209 4.3 13.3 1.0
O A:HOH500 4.4 5.9 1.0
CH2 A:TRP128 4.5 7.0 1.0
CD2 A:LEU152 4.5 5.0 1.0
CE3 A:TRP128 4.7 4.4 1.0
CG2 A:ILE209 4.9 4.7 1.0

Fluorine binding site 3 out of 6 in 5yas

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Fluorine binding site 3 out of 6 in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Hydroxynitrile Lyase Complexed with Hexafluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:30.6
occ:1.00
 F3 A:FAC300 0.0 30.6 1.0
C1 A:FAC300 1.4 30.9 1.0
F1 A:FAC300 2.2 32.7 1.0
F2 A:FAC300 2.2 30.6 1.0
C A:FAC300 2.3 32.5 1.0
O2 A:FAC300 2.7 29.9 1.0
O A:HOH500 2.7 5.9 1.0
O1 A:FAC300 2.9 31.0 1.0
CD1 A:ILE209 3.0 13.3 1.0
CD2 A:LEU157 3.4 3.2 1.0
NE2 A:HIS235 3.4 4.4 1.0
CG A:LEU157 3.4 4.4 1.0
OG A:SER80 3.5 7.4 1.0
C2 A:FAC300 3.7 33.9 1.0
CD2 A:HIS235 3.9 4.0 1.0
CD1 A:LEU157 3.9 3.3 1.0
F4 A:FAC300 4.1 33.4 1.0
F6 A:FAC300 4.2 35.4 1.0
CE1 A:HIS235 4.3 2.8 1.0
CG1 A:ILE209 4.4 7.2 1.0
F5 A:FAC300 4.5 39.1 1.0
CB A:SER80 4.5 4.4 1.0
CE1 A:PHE210 4.6 2.7 1.0
CG2 A:ILE209 4.8 4.7 1.0
CB A:LEU157 4.8 2.4 1.0
CB A:ILE209 4.9 6.4 1.0
CG A:HIS235 4.9 2.9 1.0

Fluorine binding site 4 out of 6 in 5yas

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Fluorine binding site 4 out of 6 in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Hydroxynitrile Lyase Complexed with Hexafluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:33.4
occ:1.00
 F4 A:FAC300 0.0 33.4 1.0
C2 A:FAC300 1.4 33.9 1.0
F5 A:FAC300 2.2 39.1 1.0
F6 A:FAC300 2.3 35.4 1.0
C A:FAC300 2.4 32.5 1.0
F1 A:FAC300 2.7 32.7 1.0
O2 A:FAC300 2.7 29.9 1.0
C1 A:FAC300 3.0 30.9 1.0
SG A:CYS81 3.2 13.2 1.0
O1 A:FAC300 3.6 31.0 1.0
CH2 A:TRP128 3.6 7.0 1.0
CD2 A:LEU178 3.8 12.7 1.0
F2 A:FAC300 3.8 30.6 1.0
CZ3 A:TRP128 3.9 6.7 1.0
CG1 A:ILE12 4.1 10.5 1.0
F3 A:FAC300 4.1 30.6 1.0
CD1 A:ILE12 4.3 16.4 1.0
OG A:SER80 4.6 7.4 1.0
OG1 A:THR11 4.7 5.2 1.0
CB A:CYS81 4.7 8.1 1.0
CG A:LEU178 4.7 10.7 1.0
CZ2 A:TRP128 4.9 11.6 1.0

Fluorine binding site 5 out of 6 in 5yas

Go back to Fluorine Binding Sites List in 5yas
Fluorine binding site 5 out of 6 in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Hydroxynitrile Lyase Complexed with Hexafluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:39.1
occ:1.00
 F5 A:FAC300 0.0 39.1 1.0
C2 A:FAC300 1.3 33.9 1.0
F6 A:FAC300 2.2 35.4 1.0
C A:FAC300 2.2 32.5 1.0
F4 A:FAC300 2.2 33.4 1.0
O1 A:FAC300 2.5 31.0 1.0
O2 A:FAC300 2.6 29.9 1.0
CG1 A:ILE12 2.7 10.5 1.0
O A:ILE12 3.1 3.8 1.0
CD1 A:ILE12 3.2 16.4 1.0
C1 A:FAC300 3.6 30.9 1.0
OG1 A:THR11 3.7 5.2 1.0
C A:ILE12 3.7 2.8 1.0
N A:ILE12 3.7 3.8 1.0
CB A:ILE12 3.8 8.7 1.0
SG A:CYS81 3.9 13.2 1.0
CA A:ILE12 3.9 4.1 1.0
F1 A:FAC300 4.1 32.7 1.0
F2 A:FAC300 4.1 30.6 1.0
CG2 A:THR11 4.3 2.0 1.0
F3 A:FAC300 4.5 30.6 1.0
CB A:THR11 4.6 2.7 1.0
CG2 A:ILE12 4.7 5.9 1.0
C A:THR11 4.7 3.3 1.0
CB A:CYS81 4.7 8.1 1.0
CD1 A:LEU148 4.7 4.0 1.0
CD2 A:LEU178 4.7 12.7 1.0
N A:CYS13 4.8 2.0 1.0
SG A:CYS13 5.0 5.3 1.0

Fluorine binding site 6 out of 6 in 5yas

Go back to Fluorine Binding Sites List in 5yas
Fluorine binding site 6 out of 6 in the Hydroxynitrile Lyase Complexed with Hexafluoroacetone


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Hydroxynitrile Lyase Complexed with Hexafluoroacetone within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F300

b:35.4
occ:1.00
 F6 A:FAC300 0.0 35.4 1.0
C2 A:FAC300 1.4 33.9 1.0
F5 A:FAC300 2.2 39.1 1.0
F4 A:FAC300 2.3 33.4 1.0
C A:FAC300 2.4 32.5 1.0
F2 A:FAC300 2.8 30.6 1.0
O1 A:FAC300 2.8 31.0 1.0
C1 A:FAC300 2.9 30.9 1.0
CD2 A:LEU148 3.2 3.4 1.0
CZ3 A:TRP128 3.3 6.7 1.0
F1 A:FAC300 3.3 32.7 1.0
O2 A:FAC300 3.6 29.9 1.0
CD1 A:LEU148 3.8 4.0 1.0
CH2 A:TRP128 3.8 7.0 1.0
CD1 A:ILE12 4.0 16.4 1.0
CG A:LEU148 4.0 5.7 1.0
F3 A:FAC300 4.2 30.6 1.0
CD1 A:LEU146 4.2 11.6 1.0
CG1 A:ILE12 4.2 10.5 1.0
CE3 A:TRP128 4.3 4.4 1.0
O A:ILE12 4.5 3.8 1.0
SG A:CYS13 4.9 5.3 1.0

Reference:

J.Zuegg, K.Gruber, M.Gugganig, U.G.Wagner, C.Kratky. Three-Dimensional Structures of Enzyme-Substrate Complexes of the Hydroxynitrile Lyase From Hevea Brasiliensis. Protein Sci. V. 8 1990 1999.
ISSN: ISSN 0961-8368
PubMed: 10548044
DOI: 10.1110/PS.8.10.1990
Page generated: Sun Dec 13 12:43:10 2020

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