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

The structure of Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form, PDB code: 4psp 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)	41.23 / 1.56
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	53.871, 75.887, 80.845, 105.91, 107.23, 106.75
R / Rfree (%)	13.5 / 16.9

The binding sites of Sodium atom in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Open Form (pdb code 4psp). 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 Open Form, PDB code: 4psp:
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 Open 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 Open Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na619 b:16.1 occ:1.00 O A:THR281 2.3 14.6 1.0 O A:HIS17 2.4 15.2 1.0 O A:HOH782 2.4 21.8 1.0 O A:HOH886 2.4 23.3 1.0 O A:HOH745 2.5 14.1 1.0 O A:ASP15 2.5 17.2 1.0 HA A:ASN18 3.4 16.7 1.0 C A:HIS17 3.4 10.8 1.0 C A:THR281 3.4 18.5 1.0 HA A:SER282 3.6 15.5 1.0 C A:ASP15 3.7 15.3 1.0 H A:ALA19 3.7 15.6 1.0 HB A:THR281 3.8 19.0 1.0 HA A:LYS16 3.9 22.0 1.0 C A:LYS16 3.9 16.3 1.0 N A:HIS17 4.1 15.7 1.0 O A:LYS16 4.1 19.1 1.0 HB3 A:SER282 4.2 18.4 1.0 CA A:ASN18 4.2 13.9 1.0 N A:ASN18 4.2 13.6 1.0 HA A:THR281 4.2 14.9 1.0 O A:HOH1302 4.3 41.1 1.0 CA A:LYS16 4.3 18.4 1.0 CA A:SER282 4.3 12.9 1.0 O A:HOH1321 4.3 33.8 1.0 N A:SER282 4.3 14.2 1.0 N A:ALA19 4.3 13.0 1.0 CA A:THR281 4.3 12.4 1.0 O A:HOH1043 4.3 25.2 1.0 H A:HIS17 4.3 18.9 1.0 O A:HOH736 4.4 14.6 1.0 CA A:HIS17 4.4 14.2 1.0 HB2 A:ALA19 4.4 15.1 1.0 N A:LYS16 4.4 14.3 1.0 CB A:THR281 4.5 15.8 1.0 HA A:ASP15 4.5 19.5 1.0 O A:HOH1469 4.6 36.0 1.0 O A:HOH1005 4.7 30.5 1.0 CB A:SER282 4.7 15.3 1.0 C A:ASN18 4.7 12.4 1.0 CA A:ASP15 4.7 16.2 1.0 HB3 A:HIS17 4.9 16.9 1.0 HB3 A:ASP15 4.9 24.6 1.0 H A:ASN18 5.0 16.3 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Open 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 Open Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:15.3 occ:1.00 O B:HOH747 2.4 12.4 1.0 O B:HOH833 2.4 22.4 1.0 O B:GLU72 2.4 18.7 1.0 O B:HOH1193 2.4 25.2 1.0 O B:HOH1217 2.5 19.6 1.0 O B:HOH1034 2.5 22.1 1.0 C B:GLU72 3.5 15.2 1.0 H B:GLY74 3.7 15.3 1.0 HD21 B:ASN77 3.8 17.6 1.0 HA B:GLU72 3.9 19.8 1.0 HA B:TRP73 3.9 17.8 1.0 O B:HOH1102 4.1 25.6 1.0 O B:HOH877 4.2 19.4 1.0 CA B:GLU72 4.3 16.5 1.0 O B:HOH813 4.3 19.0 1.0 N B:TRP73 4.4 13.5 1.0 O B:HOH1270 4.5 33.5 1.0 OD1 B:ASN77 4.5 13.8 1.0 ND2 B:ASN77 4.5 14.7 1.0 N B:GLY74 4.5 12.8 1.0 OE2 B:GLU76 4.5 14.7 1.0 CA B:TRP73 4.6 14.8 1.0 O B:GLU71 4.8 18.0 1.0 CG B:ASN77 5.0 13.3 1.0 HB3 B:GLU72 5.0 29.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of GH29 Family Alpha-L-Fucosidase From Fusarium Graminearum in the Open 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 Open Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na606 b:12.8 occ:1.00 O B:THR281 2.3 14.5 1.0 O B:HIS17 2.3 12.4 1.0 O B:ASP15 2.4 14.5 1.0 O B:HOH863 2.5 19.0 1.0 O B:HOH718 2.5 11.7 1.0 O B:HOH819 2.5 20.9 1.0 C B:HIS17 3.4 8.8 1.0 C B:THR281 3.4 9.3 1.0 HA B:SER282 3.5 12.3 1.0 HA B:ASN18 3.6 14.4 1.0 C B:ASP15 3.6 14.8 1.0 HB B:THR281 3.7 15.3 1.0 H B:ALA19 3.7 12.4 1.0 C B:LYS16 3.8 14.2 0.6 HA B:LYS16 3.8 18.2 0.5 HA B:LYS16 3.8 18.3 0.6 O B:LYS16 3.9 15.0 0.6 C B:LYS16 4.0 14.1 0.5 N B:HIS17 4.0 12.9 1.0 HA B:THR281 4.2 12.3 1.0 HB3 B:SER282 4.2 13.8 1.0 O B:HOH1374 4.2 36.5 1.0 CA B:LYS16 4.2 15.2 0.6 H B:HIS17 4.2 15.5 0.5 CA B:LYS16 4.2 15.2 0.5 N B:ASN18 4.2 11.7 1.0 O B:HOH1437 4.2 41.1 1.0 CA B:ASN18 4.3 12.0 1.0 CA B:THR281 4.3 10.2 1.0 CA B:SER282 4.3 10.2 1.0 N B:SER282 4.3 9.4 1.0 H B:HIS17 4.3 15.5 0.6 N B:LYS16 4.3 13.1 0.6 N B:LYS16 4.3 13.2 0.5 O B:HOH1013 4.3 28.3 1.0 N B:ALA19 4.3 10.3 1.0 CA B:HIS17 4.4 11.0 1.0 O B:LYS16 4.4 13.3 0.5 O B:HOH1029 4.4 12.7 1.0 HB2 B:ALA19 4.4 15.3 1.0 CB B:THR281 4.5 12.7 1.0 HA B:ASP15 4.5 16.3 1.0 O B:HOH1000 4.7 24.1 1.0 CA B:ASP15 4.7 13.6 1.0 CB B:SER282 4.7 11.5 1.0 O B:HOH1081 4.7 35.5 1.0 C B:ASN18 4.8 11.1 1.0 HB3 B:ASP15 4.9 18.8 1.0 HB3 B:HIS17 5.0 13.2 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