Atomistry » Fluorine » PDB 5y6d-5zab » 5yas
Atomistry »
  Fluorine »
    PDB 5y6d-5zab »
      5yas »

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

Go back to Fluorine Binding Sites List in 5yas
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

Go back to Fluorine Binding Sites List in 5yas
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

Go back to Fluorine Binding Sites List in 5yas
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: Thu Aug 1 17:10:12 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