Sodium in PDB 1w9w: Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose

The structure of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose, PDB code: 1w9w was solved by A.B.Boraston, A.L.Van Bueren, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 2.1
Space group	P 43 21 2
Cell size a, b, c (Å), α, β, γ (°)	61.551, 61.551, 121.711, 90.00, 90.00, 90.00
R / Rfree (%)	20.5 / 26.7

The binding sites of Sodium atom in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose (pdb code 1w9w). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose, PDB code: 1w9w:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na900 b:34.1 occ:1.00 O A:TRP42 2.2 41.0 1.0 O A:GLY25 2.3 40.4 1.0 OD1 A:ASN44 2.3 45.3 1.0 OD2 A:ASP47 2.4 34.2 1.0 O A:HOH2052 2.4 48.9 1.0 C A:TRP42 3.4 41.4 1.0 C A:GLY25 3.4 39.7 1.0 CG A:ASN44 3.4 45.2 1.0 CG A:ASP47 3.5 36.6 1.0 N A:ASN44 3.7 43.8 1.0 OD1 A:ASP47 3.9 38.5 1.0 CB A:ASN44 3.9 44.2 1.0 CA A:GLY25 4.0 38.9 1.0 CA A:ILE43 4.0 41.9 1.0 C A:ILE43 4.1 43.2 1.0 N A:ILE43 4.1 41.2 1.0 O A:HOH2100 4.2 56.0 1.0 CA A:ASN44 4.5 43.9 1.0 N A:ILE26 4.5 39.5 1.0 CA A:TRP42 4.5 41.6 1.0 CB A:TRP42 4.5 42.0 1.0 ND2 A:ASN44 4.6 48.6 1.0 CA A:ILE26 4.7 39.9 1.0 CB A:ASP47 4.8 39.7 1.0 O A:ILE43 4.9 42.6 1.0

Sodium binding site 2 out of 2 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Laminarihexaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:43.1 occ:1.00 OD1 A:ASN134 2.2 48.4 1.0 OE1 A:GLU18 2.2 51.3 1.0 O A:HOH2040 2.3 58.0 1.0 OE1 A:GLN16 2.4 46.0 1.0 O A:ASP38 2.5 49.8 1.0 O A:ASN134 2.5 43.8 1.0 CD A:GLU18 2.9 54.1 1.0 OE2 A:GLU18 2.9 56.3 1.0 CG A:ASN134 3.3 45.5 1.0 C A:ASN134 3.5 43.4 1.0 CD A:GLN16 3.6 43.8 1.0 C A:ASP38 3.7 50.2 1.0 CA A:ASN134 4.0 43.7 1.0 CB A:GLN16 4.1 43.0 1.0 N A:ASP38 4.2 55.4 1.0 ND2 A:ASN134 4.2 42.4 1.0 CB A:ASN134 4.2 43.6 1.0 CG A:GLN16 4.3 43.6 1.0 CG A:GLU18 4.4 43.1 1.0 O A:HOH2018 4.4 57.2 1.0 O A:HOH2017 4.5 59.9 1.0 CA A:ASP38 4.5 53.0 1.0 CA A:GLN16 4.5 43.1 1.0 O A:GLY36 4.6 59.7 1.0 O A:HOH2039 4.6 59.2 1.0 N A:ALA17 4.6 42.3 1.0 N A:TRP135 4.6 43.5 1.0 N A:ASN39 4.6 47.8 1.0 NE2 A:GLN16 4.7 47.0 1.0 CA A:ASN39 4.8 46.1 1.0 CD1 A:TRP135 4.8 50.1 1.0 CB A:TRP135 4.9 45.1 1.0 C A:GLY37 4.9 57.0 1.0

A.L.Van Bueren, C.Moreland, H.J.Gilbert, A.B.Boraston. Family 6 Carbohydrate Binding Modules Recognize the Non-Reducing End of Beta-1,3-Linked Glucans By Presenting A Unique Ligand Binding Surface J.Biol.Chem. V. 280 530 2005.
ISSN: ISSN 0021-9258
PubMed: 15501830
DOI: 10.1074/JBC.M410113200