Fluorine in PDB 1xsk: Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate

The structure of Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate, PDB code: 1xsk was solved by A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, N.C.Strynadka, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.88 / 2.20
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	162.142, 175.465, 210.854, 90.00, 90.00, 90.00
R / Rfree (%)	23.5 / 27.2

The binding sites of Fluorine atom in the Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate (pdb code 1xsk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate, PDB code: 1xsk:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ A:F801 b:39.6 occ:1.00 F5 A:XYF801 0.0 39.6 1.0 C5 A:XYF801 1.4 38.3 1.0 O5 A:XYF801 2.3 36.5 1.0 C4 A:XYF801 2.4 38.2 1.0 O4 A:XYF801 3.0 37.8 1.0 SG A:CYS307 3.1 40.8 1.0 C1 A:XYF801 3.1 35.7 1.0 OD2 A:ASP416 3.3 28.5 1.0 CE1 A:PHE277 3.4 35.4 1.0 NE1 A:TRP345 3.4 18.4 1.0 CH2 A:TRP380 3.6 27.0 1.0 C3 A:XYF801 3.7 36.9 1.0 CZ A:PHE277 3.7 34.5 1.0 CD1 A:PHE277 3.7 34.7 1.0 OD2 A:ASP306 3.8 34.5 1.0 C2 A:XYF801 4.0 36.2 1.0 CZ2 A:TRP380 4.1 26.6 1.0 CD1 A:TRP345 4.1 19.2 1.0 CE1 A:PHE417 4.1 21.5 1.0 CE2 A:TRP345 4.1 20.2 1.0 CE2 A:PHE277 4.3 34.9 1.0 CG A:PHE277 4.3 35.5 1.0 CZ2 A:TRP345 4.5 19.8 1.0 CZ A:PHE417 4.5 23.5 1.0 CG A:ASP416 4.5 26.4 1.0 CD2 A:PHE277 4.5 35.5 1.0 CZ3 A:TRP380 4.6 27.5 1.0 CG A:ASP306 4.7 34.2 1.0 O3 A:XYF801 4.8 38.3 1.0 CB A:CYS307 4.8 30.6 1.0 OD1 A:ASP306 4.8 35.2 1.0

Fluorine binding site 2 out of 4 in the Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ B:F802 b:45.1 occ:1.00 F5 B:XYF802 0.0 45.1 1.0 C5 B:XYF802 1.4 43.2 1.0 O5 B:XYF802 2.3 41.8 1.0 C4 B:XYF802 2.4 42.5 1.0 O4 B:XYF802 3.0 41.0 1.0 NE1 B:TRP345 3.1 32.0 1.0 OD2 B:ASP416 3.2 35.5 1.0 SG B:CYS307 3.2 41.6 1.0 C1 B:XYF802 3.2 39.5 1.0 CE1 B:PHE277 3.5 44.9 1.0 OD2 B:ASP306 3.7 45.9 1.0 C3 B:XYF802 3.7 41.9 1.0 CH2 B:TRP380 3.7 35.5 1.0 CD1 B:PHE277 3.8 45.4 1.0 CD1 B:TRP345 3.8 32.9 1.0 CE2 B:TRP345 3.9 31.1 1.0 C2 B:XYF802 4.0 40.5 1.0 CE1 B:PHE417 4.1 28.4 1.0 CZ B:PHE277 4.1 44.9 1.0 CZ2 B:TRP380 4.2 34.0 1.0 CZ2 B:TRP345 4.3 30.7 1.0 CG B:ASP416 4.4 35.0 1.0 CG B:ASP306 4.6 45.2 1.0 CG B:PHE277 4.6 45.6 1.0 CZ3 B:TRP380 4.7 35.3 1.0 CZ B:PHE417 4.7 29.1 1.0 OD1 B:ASP306 4.7 43.7 1.0 O3 B:XYF802 4.8 43.8 1.0 CG B:TRP345 4.8 33.6 1.0 CB B:CYS307 4.9 38.5 1.0 CD2 B:TRP345 4.9 31.8 1.0 CE2 B:PHE277 4.9 44.5 1.0

Fluorine binding site 3 out of 4 in the Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ C:F803 b:38.3 occ:1.00 F5 C:XYF803 0.0 38.3 1.0 C5 C:XYF803 1.4 37.6 1.0 O5 C:XYF803 2.3 35.1 1.0 C4 C:XYF803 2.4 37.9 1.0 O4 C:XYF803 3.0 37.4 1.0 SG C:CYS307 3.1 37.1 1.0 NE1 C:TRP345 3.1 20.0 1.0 C1 C:XYF803 3.1 33.7 1.0 OD2 C:ASP416 3.2 27.2 1.0 CE1 C:PHE277 3.5 42.1 1.0 CH2 C:TRP380 3.6 26.9 1.0 C3 C:XYF803 3.6 36.6 1.0 OD2 C:ASP306 3.7 34.8 1.0 CD1 C:PHE277 3.8 41.7 1.0 CD1 C:TRP345 3.8 17.3 1.0 CZ2 C:TRP380 4.0 27.1 1.0 CE2 C:TRP345 4.0 18.9 1.0 C2 C:XYF803 4.0 36.2 1.0 CZ C:PHE277 4.1 42.1 1.0 CE1 C:PHE417 4.1 21.4 1.0 CZ2 C:TRP345 4.4 20.2 1.0 CG C:PHE277 4.5 41.5 1.0 CG C:ASP416 4.5 26.7 1.0 CG C:ASP306 4.6 31.2 1.0 CZ3 C:TRP380 4.6 25.6 1.0 CZ C:PHE417 4.7 22.3 1.0 CE2 C:PHE277 4.7 43.3 1.0 O3 C:XYF803 4.8 40.0 1.0 CB C:CYS307 4.8 28.8 1.0 CG C:TRP345 4.9 18.5 1.0 OD1 C:ASP306 4.9 28.6 1.0 CD2 C:PHE277 4.9 42.9 1.0 CD2 C:TRP345 5.0 18.4 1.0

Fluorine binding site 4 out of 4 in the Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of A Family 31 Alpha Glycosidase Glycosyl-Enzyme Intermediate within 5.0Å range: probe atom residue distance (Å) B Occ E:F804 b:29.4 occ:0.50 F5 E:XYF804 0.0 29.4 0.5 C5 E:XYF804 1.4 27.6 0.5 O5 E:XYF804 2.3 27.1 0.5 C4 E:XYF804 2.4 26.7 0.5 O4 E:XYF804 3.0 25.5 0.5 SG E:CYS307 3.1 43.4 1.0 C1 E:XYF804 3.2 26.1 0.5 CE1 E:PHE277 3.3 51.4 1.0 OD2 E:ASP416 3.3 24.2 1.0 CH2 E:TRP380 3.5 38.6 1.0 CD1 E:PHE277 3.6 49.8 1.0 NE1 E:TRP345 3.6 30.0 1.0 C3 E:XYF804 3.7 25.5 0.5 CZ E:PHE277 3.9 51.0 1.0 CZ2 E:TRP380 4.0 38.0 1.0 CE1 E:PHE417 4.0 25.5 1.0 C2 E:XYF804 4.0 25.3 0.5 OD2 E:ASP306 4.1 42.3 1.0 CZ E:PHE417 4.2 25.6 1.0 CE2 E:TRP345 4.3 29.8 1.0 CD1 E:TRP345 4.3 27.4 1.0 CG E:PHE277 4.4 50.2 1.0 CZ3 E:TRP380 4.5 38.6 1.0 CG E:ASP416 4.6 25.0 1.0 CZ2 E:TRP345 4.6 29.5 1.0 CE2 E:PHE277 4.6 51.0 1.0 O3 E:XYF804 4.8 26.1 0.5 CB E:CYS307 4.8 32.8 1.0 CD2 E:PHE277 4.8 50.7 1.0 CG E:ASP306 4.9 40.1 1.0 OD1 E:ASP306 5.0 39.4 1.0

A.L.Lovering, S.S.Lee, Y.W.Kim, S.G.Withers, N.C.Strynadka. Mechanistic and Structural Analysis of A Family 31 {Alpha}-Glycosidase and Its Glycosyl-Enzyme Intermediate J.Biol.Chem. V. 280 2105 2005.
ISSN: ISSN 0021-9258
PubMed: 15501829
DOI: 10.1074/JBC.M410468200