Sodium in PDB 4ni3: Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form

The structure of Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form, PDB code: 4ni3 was solved by H.Cao, J.D.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)	37.93 / 1.40
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.511, 75.512, 80.367, 105.61, 107.19, 106.71
R / Rfree (%)	14.5 / 16.7

The binding sites of Sodium atom in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form (pdb code 4ni3). 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 GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form, PDB code: 4ni3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form


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 GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na620 b:20.6 occ:1.00 O A:HIS17 2.3 17.7 1.0 O A:THR281 2.4 19.7 1.0 O A:HOH795 2.4 25.4 1.0 O A:HOH1104 2.4 27.7 1.0 O A:ASP15 2.5 21.5 1.0 O A:HOH734 2.5 17.7 1.0 C A:HIS17 3.4 16.1 1.0 C A:THR281 3.4 19.8 1.0 C A:ASP15 3.7 19.6 1.0 C A:LYS16 3.9 19.5 1.0 N A:HIS17 4.0 19.6 1.0 O A:LYS16 4.1 23.4 1.0 N A:ASN18 4.2 17.0 1.0 CA A:ASN18 4.2 17.8 1.0 O A:HOH904 4.3 33.0 1.0 CA A:LYS16 4.3 20.4 1.0 CA A:SER282 4.3 17.6 1.0 CA A:THR281 4.3 19.1 1.0 N A:SER282 4.3 16.7 1.0 CA A:HIS17 4.3 17.9 1.0 N A:ALA19 4.3 17.1 1.0 N A:LYS16 4.4 20.5 1.0 O A:HOH735 4.4 19.3 1.0 CB A:THR281 4.5 20.1 1.0 O A:HOH1147 4.5 40.6 1.0 O A:HOH1028 4.6 36.0 1.0 CB A:SER282 4.7 18.4 1.0 CA A:ASP15 4.7 18.7 1.0 C A:ASN18 4.7 18.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form


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 GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na608 b:22.0 occ:1.00 O B:HOH1256 2.3 26.4 1.0 O B:HOH948 2.4 25.8 1.0 O B:HOH740 2.4 18.5 1.0 O B:HOH1317 2.4 31.4 1.0 O B:GLU72 2.4 22.2 1.0 O B:HOH1304 2.5 26.7 1.0 C B:GLU72 3.5 20.3 1.0 O B:HOH1188 4.1 35.8 1.0 O B:HOH789 4.2 23.3 1.0 CA B:GLU72 4.3 22.2 1.0 O B:HOH1112 4.4 25.6 1.0 N B:TRP73 4.4 18.6 1.0 OD1 B:ASN77 4.5 18.2 1.0 ND2 B:ASN77 4.5 18.1 1.0 N B:GLY74 4.5 15.9 1.0 OE2 B:GLU76 4.5 18.2 1.0 CA B:TRP73 4.6 16.8 1.0 O B:HOH1081 4.7 37.4 1.0 CG B:ASN77 4.9 16.2 1.0 O B:GLU71 5.0 22.5 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form


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 GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Closed Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na609 b:18.7 occ:1.00 O B:THR281 2.3 18.9 1.0 O B:HOH1114 2.3 26.3 1.0 O B:HIS17 2.3 18.1 1.0 O B:HOH1177 2.4 29.3 1.0 O B:ASP15 2.4 21.7 1.0 O B:HOH730 2.5 17.7 1.0 C B:HIS17 3.4 16.7 1.0 C B:THR281 3.4 17.5 1.0 C B:ASP15 3.6 20.2 1.0 C B:LYS16 3.8 24.4 1.0 N B:HIS17 4.0 18.1 1.0 O B:LYS16 4.0 24.1 1.0 N B:ASN18 4.2 15.7 1.0 CA B:LYS16 4.2 21.4 1.0 CA B:ASN18 4.3 16.7 1.0 CA B:SER282 4.3 15.3 1.0 CA B:HIS17 4.3 16.8 1.0 CA B:THR281 4.3 17.0 1.0 N B:SER282 4.3 15.1 1.0 N B:ALA19 4.3 14.3 1.0 N B:LYS16 4.3 20.6 1.0 O B:HOH1176 4.4 18.9 1.0 O B:HOH879 4.4 37.2 1.0 CB B:THR281 4.5 17.9 1.0 CA B:ASP15 4.7 18.7 1.0 CB B:SER282 4.7 17.5 1.0 O B:HOH974 4.7 40.6 1.0 O B:HOH1123 4.8 40.3 1.0 C B:ASN18 4.8 15.6 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