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Fluorine in PDB 4b0p: Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium

Enzymatic activity of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium

All present enzymatic activity of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium:
3.1.1.8;

Protein crystallography data

The structure of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium, PDB code: 4b0p was solved by M.Wandhammer, M.De Koning, M.Van Grol, D.Noort, M.Goeldner, F.Nachon, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.878 / 2.50
Space group I 4 2 2
Cell size a, b, c (Å), α, β, γ (°) 154.230, 154.230, 133.860, 90.00, 90.00, 90.00
R / Rfree (%) 16.44 / 21.2

Other elements in 4b0p:

The structure of Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium also contains other interesting chemical elements:

Potassium (K) 1 atom
Calcium (Ca) 4 atoms
Chlorine (Cl) 4 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium (pdb code 4b0p). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 5 binding sites of Fluorine where determined in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium, PDB code: 4b0p:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5;

Fluorine binding site 1 out of 5 in 4b0p

Go back to Fluorine Binding Sites List in 4b0p
Fluorine binding site 1 out of 5 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


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 Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1179

b:73.5
occ:1.00
 FAE A:MF51179 0.0 73.5 1.0
CAS A:MF51179 1.3 74.6 1.0
CAQ A:MF51179 2.3 71.5 1.0
CAU A:MF51179 2.3 77.6 1.0
FAC A:MF51179 2.7 66.3 1.0
CAL A:MF51179 2.7 83.2 1.0
OAN A:MF51179 3.0 84.3 1.0
CB A:ASP70 3.0 45.2 0.5
CG A:ASP70 3.0 41.5 0.5
OD2 A:ASP70 3.1 34.0 0.5
CB A:ASP70 3.1 48.6 0.5
O A:HOH3041 3.5 48.2 1.0
CAP A:MF51179 3.5 71.3 1.0
CAT A:MF51179 3.6 72.3 1.0
CG A:ASP70 3.6 45.1 0.5
OD1 A:ASP70 3.7 41.8 0.5
OH A:TYR332 3.8 47.0 1.0
CE2 A:TYR332 3.9 37.0 1.0
CZ A:TYR332 4.0 41.1 1.0
OD2 A:ASP70 4.0 44.6 0.5
CAR A:MF51179 4.0 72.8 1.0
OD1 A:ASP70 4.2 44.1 0.5
NAM A:MF51179 4.2 74.0 1.0
CA A:ASP70 4.3 49.3 0.5
CA A:ASP70 4.5 49.4 0.5
FAB A:MF51179 4.6 71.1 1.0
FAF A:MF51179 4.7 69.7 1.0
O A:HOH3064 4.7 65.1 1.0
CD2 A:TYR332 4.7 37.6 1.0
CE1 A:TYR332 4.9 38.0 1.0
CAG A:MF51179 4.9 59.9 1.0
N A:ASP70 4.9 48.9 1.0

Fluorine binding site 2 out of 5 in 4b0p

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Fluorine binding site 2 out of 5 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


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 Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1179

b:66.3
occ:1.00
 FAC A:MF51179 0.0 66.3 1.0
CAQ A:MF51179 1.4 71.5 1.0
CAS A:MF51179 2.4 74.6 1.0
CAP A:MF51179 2.4 71.3 1.0
FAE A:MF51179 2.7 73.5 1.0
FAB A:MF51179 2.7 71.1 1.0
O A:HOH3101 3.5 51.8 1.0
OD2 A:ASP70 3.6 44.6 0.5
CAU A:MF51179 3.6 77.6 1.0
CAR A:MF51179 3.6 72.8 1.0
CD2 A:TYR332 3.7 37.6 1.0
CE2 A:TYR332 3.7 37.0 1.0
CG A:ASP70 4.0 45.1 0.5
CAT A:MF51179 4.1 72.3 1.0
CG A:TYR332 4.3 38.5 1.0
CB A:ASP70 4.3 48.6 0.5
CZ A:TYR332 4.3 41.1 1.0
O A:HOH3064 4.5 65.1 1.0
OD1 A:ASP70 4.7 44.1 0.5
FAD A:MF51179 4.8 77.9 1.0
CAL A:MF51179 4.8 83.2 1.0
CG A:ASP70 4.8 41.5 0.5
OD1 A:ASP70 4.8 41.8 0.5
CD1 A:TYR332 4.8 37.2 1.0
CB A:ASP70 4.8 45.2 0.5
CE1 A:TYR332 4.8 38.0 1.0
O A:PRO285 4.9 57.7 1.0
OH A:TYR332 4.9 47.0 1.0
CB A:TYR332 5.0 42.3 1.0

Fluorine binding site 3 out of 5 in 4b0p

Go back to Fluorine Binding Sites List in 4b0p
Fluorine binding site 3 out of 5 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


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 Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1179

b:71.1
occ:1.00
 FAB A:MF51179 0.0 71.1 1.0
CAP A:MF51179 1.3 71.3 1.0
CAQ A:MF51179 2.3 71.5 1.0
CAR A:MF51179 2.4 72.8 1.0
FAC A:MF51179 2.7 66.3 1.0
FAD A:MF51179 2.7 77.9 1.0
O A:HOH3101 3.5 51.8 1.0
CG A:TYR332 3.5 38.5 1.0
O A:PRO285 3.5 57.7 1.0
CD1 A:PHE329 3.6 29.0 1.0
CAS A:MF51179 3.6 74.6 1.0
CAT A:MF51179 3.6 72.3 1.0
CD1 A:TYR332 3.7 37.2 1.0
CB A:TYR332 3.8 42.3 1.0
CD2 A:TYR332 3.9 37.6 1.0
CE1 A:PHE329 4.0 27.1 1.0
CAU A:MF51179 4.1 77.6 1.0
CE1 A:TYR332 4.3 38.0 1.0
C A:PRO285 4.4 48.9 1.0
CE2 A:TYR332 4.4 37.0 1.0
CB A:PRO285 4.5 46.0 1.0
CZ A:TYR332 4.6 41.1 1.0
CG A:PHE329 4.6 32.3 1.0
CA A:PHE329 4.6 38.0 1.0
FAE A:MF51179 4.6 73.5 1.0
CA A:PRO285 4.7 51.9 1.0
FAF A:MF51179 4.7 69.7 1.0
CB A:PHE329 4.9 37.8 1.0

Fluorine binding site 4 out of 5 in 4b0p

Go back to Fluorine Binding Sites List in 4b0p
Fluorine binding site 4 out of 5 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


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 Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1179

b:77.9
occ:1.00
 FAD A:MF51179 0.0 77.9 1.0
CAR A:MF51179 1.3 72.8 1.0
CAT A:MF51179 2.4 72.3 1.0
CAP A:MF51179 2.4 71.3 1.0
FAF A:MF51179 2.7 69.7 1.0
FAB A:MF51179 2.7 71.1 1.0
CD1 A:PHE329 3.3 29.0 1.0
O A:ALA328 3.4 48.8 1.0
C A:ALA328 3.5 43.4 1.0
CE1 A:PHE329 3.5 27.1 1.0
CD1 A:TYR332 3.6 37.2 1.0
CA A:PHE329 3.6 38.0 1.0
CAU A:MF51179 3.6 77.6 1.0
CAQ A:MF51179 3.6 71.5 1.0
N A:PHE329 3.6 39.7 1.0
CG A:PHE329 3.7 32.3 1.0
CE1 A:TYR332 3.7 38.0 1.0
CB A:ALA328 3.8 34.2 1.0
CZ A:PHE329 4.1 27.3 1.0
CAS A:MF51179 4.1 74.6 1.0
CB A:PHE329 4.2 37.8 1.0
CD2 A:PHE329 4.2 30.3 1.0
CA A:ALA328 4.3 36.5 1.0
CG A:TYR332 4.4 38.5 1.0
CE2 A:PHE329 4.4 26.9 1.0
CZ A:TYR332 4.6 41.1 1.0
FAC A:MF51179 4.8 66.3 1.0
CAL A:MF51179 4.8 83.2 1.0
C A:PHE329 4.8 35.5 1.0
CB A:TYR332 5.0 42.3 1.0

Fluorine binding site 5 out of 5 in 4b0p

Go back to Fluorine Binding Sites List in 4b0p
Fluorine binding site 5 out of 5 in the Crystal Structure of Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium


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 Soman-Aged Human Butyrylcholinesterase in Complex with Methyl 2-(Pentafluorobenzyloxyimino) Pyridinium within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1179

b:69.7
occ:1.00
 FAF A:MF51179 0.0 69.7 1.0
CAT A:MF51179 1.4 72.3 1.0
CAR A:MF51179 2.4 72.8 1.0
CAU A:MF51179 2.4 77.6 1.0
FAD A:MF51179 2.7 77.9 1.0
CAL A:MF51179 2.8 83.2 1.0
NAM A:MF51179 3.4 74.0 1.0
CAS A:MF51179 3.6 74.6 1.0
CAP A:MF51179 3.6 71.3 1.0
OAN A:MF51179 3.7 84.3 1.0
CE1 A:TYR332 3.9 38.0 1.0
CB A:ALA328 3.9 34.2 1.0
CAQ A:MF51179 4.1 71.5 1.0
OH A:TYR332 4.2 47.0 1.0
CAJ A:MF51179 4.2 42.0 1.0
CZ A:TYR332 4.3 41.1 1.0
CAG A:MF51179 4.6 59.9 1.0
O A:ALA328 4.6 48.8 1.0
CD1 A:TYR332 4.6 37.2 1.0
FAE A:MF51179 4.7 73.5 1.0
FAB A:MF51179 4.7 71.1 1.0
CZ2 A:TRP430 4.8 34.5 1.0
C A:ALA328 4.8 43.4 1.0
CAO A:MF51179 4.9 47.7 1.0
CA A:ALA328 4.9 36.5 1.0

Reference:

M.Wandhammer, M.De Koning, M.Van Grol, M.Loiodice, L.Saurel, D.Noort, M.Goeldner, F.Nachon. A Step Toward the Reactivation of Aged Cholinesterases - Crystal Structure of Ligands Binding to Aged Human Butyrylcholinesterase Chem.Biol.Interact V. 203 19 2013.
ISSN: ISSN 0009-2797
PubMed: 22922115
DOI: 10.1016/J.CBI.2012.08.005
Page generated: Thu Aug 1 00:06:39 2024

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