Sodium in PDB 4psr: Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose

The structure of Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose, PDB code: 4psr was solved by H.Cao, J.Walton, P.Brumm, G.N.Phillips Jr., with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.28 / 1.38
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	54.153, 75.989, 80.970, 105.69, 107.32, 106.93
R / Rfree (%)	13.8 / 16.6

The binding sites of Sodium atom in the Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose (pdb code 4psr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose, PDB code: 4psr:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na619 b:15.1 occ:1.00 O A:THR281 2.3 15.6 1.0 O A:HOH782 2.4 20.2 1.0 O A:HIS17 2.4 13.7 1.0 O A:ASP15 2.4 16.1 1.0 O A:HOH887 2.4 23.3 1.0 O A:HOH745 2.5 13.8 1.0 C A:THR281 3.4 15.2 1.0 C A:HIS17 3.4 12.4 1.0 HA A:ASN18 3.5 16.7 1.0 HA A:SER282 3.6 14.3 1.0 C A:ASP15 3.6 15.8 1.0 HB A:THR281 3.7 18.3 1.0 H A:ALA19 3.8 14.4 1.0 HA A:LYS16 3.9 19.1 1.0 C A:LYS16 3.9 17.2 1.0 N A:HIS17 4.1 15.3 1.0 HB3 A:SER282 4.1 17.6 1.0 HA A:THR281 4.1 13.6 1.0 O A:LYS16 4.1 17.3 1.0 N A:ASN18 4.2 12.6 1.0 CA A:ASN18 4.2 13.9 1.0 CA A:THR281 4.2 11.3 1.0 CA A:LYS16 4.3 16.0 1.0 N A:SER282 4.3 12.9 1.0 CA A:SER282 4.3 11.9 1.0 O A:HOH1065 4.3 26.3 1.0 H A:HIS17 4.3 18.3 1.0 N A:ALA19 4.4 12.0 1.0 CA A:HIS17 4.4 13.2 1.0 CB A:THR281 4.4 15.2 1.0 N A:LYS16 4.4 15.6 1.0 HA A:ASP15 4.4 18.2 1.0 HB2 A:ALA19 4.5 14.7 1.0 O A:HOH736 4.5 14.7 1.0 O A:HOH1188 4.6 32.3 1.0 CA A:ASP15 4.7 15.2 1.0 CB A:SER282 4.7 14.7 1.0 C A:ASN18 4.8 12.8 1.0 O A:HOH1021 4.8 32.6 1.0 HB3 A:ASP15 4.8 19.9 1.0 HB3 A:HIS17 4.9 15.4 1.0 H A:ASN18 5.0 15.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:17.4 occ:1.00 O B:HOH837 2.3 22.5 1.0 O B:GLU72 2.3 18.0 1.0 O B:HOH1251 2.4 23.0 1.0 O B:HOH1287 2.4 21.0 1.0 O B:HOH751 2.4 13.3 1.0 O B:HOH1055 2.5 23.5 1.0 C B:GLU72 3.4 13.6 1.0 H B:GLY74 3.7 14.1 1.0 HA B:GLU72 3.8 18.4 1.0 HD21 B:ASN77 3.8 18.3 1.0 HA B:TRP73 4.0 15.3 1.0 O B:HOH1133 4.2 28.7 1.0 O B:HOH883 4.2 19.4 1.0 CA B:GLU72 4.2 15.4 1.0 O B:HOH817 4.4 19.7 1.0 N B:TRP73 4.4 13.3 1.0 O B:HOH1363 4.5 33.6 1.0 OD1 B:ASN77 4.6 13.8 1.0 N B:GLY74 4.6 11.7 1.0 ND2 B:ASN77 4.6 15.3 1.0 OE2 B:GLU76 4.6 14.9 1.0 CA B:TRP73 4.6 12.8 1.0 O B:GLU71 4.9 17.6 1.0 HB3 B:GLU72 4.9 22.8 1.0 CG B:ASN77 5.0 12.6 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form in Complex with L-Fucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:13.4 occ:1.00 O B:THR281 2.3 13.7 1.0 O B:ASP15 2.4 15.1 1.0 O B:HIS17 2.4 12.4 1.0 O B:HOH867 2.4 20.3 1.0 O B:HOH823 2.5 20.8 1.0 O B:HOH722 2.5 12.3 1.0 C B:HIS17 3.4 12.2 1.0 C B:THR281 3.4 10.6 1.0 HA B:ASN18 3.5 14.2 1.0 HA B:SER282 3.6 12.8 1.0 C B:ASP15 3.6 14.5 1.0 HB B:THR281 3.7 14.8 1.0 H B:ALA19 3.7 12.4 1.0 C B:LYS16 3.8 12.9 0.6 HA B:LYS16 3.8 17.8 0.4 HA B:LYS16 3.9 17.8 0.6 O B:LYS16 3.9 12.9 0.6 N B:HIS17 4.0 12.4 1.0 C B:LYS16 4.0 12.9 0.4 HB3 B:SER282 4.1 15.1 1.0 H B:HIS17 4.1 14.9 0.4 HA B:THR281 4.2 11.9 1.0 O B:HOH1593 4.2 38.8 1.0 N B:ASN18 4.2 10.6 1.0 CA B:LYS16 4.2 14.8 0.6 CA B:ASN18 4.2 11.8 1.0 CA B:LYS16 4.2 14.8 0.4 CA B:THR281 4.3 9.9 1.0 N B:SER282 4.3 10.4 1.0 H B:HIS17 4.3 14.9 0.6 CA B:SER282 4.3 10.7 1.0 CA B:HIS17 4.3 11.2 1.0 N B:ALA19 4.4 10.3 1.0 N B:LYS16 4.4 13.8 0.4 N B:LYS16 4.4 13.7 0.6 O B:HOH1033 4.4 27.3 1.0 O B:HOH1050 4.4 13.3 1.0 CB B:THR281 4.4 12.3 1.0 HA B:ASP15 4.4 17.2 1.0 HB2 B:ALA19 4.5 14.5 1.0 O B:LYS16 4.5 16.4 0.4 CA B:ASP15 4.7 14.3 1.0 O B:HOH1019 4.7 24.6 1.0 CB B:SER282 4.7 12.6 1.0 O B:HOH1109 4.7 37.8 1.0 C B:ASN18 4.8 11.1 1.0 HB3 B:ASP15 4.8 20.7 1.0 HB3 B:HIS17 4.9 12.6 1.0 H B:ASN18 5.0 12.7 1.0

H.Cao, J.D.Walton, P.Brumm, G.N.Phillips. Structure and Substrate Specificity of A Eukaryotic Fucosidase From Fusarium Graminearum. J.Biol.Chem. V. 289 25624 2014.
ISSN: ISSN 0021-9258
PubMed: 25086049
DOI: 10.1074/JBC.M114.583286