Sodium in PDB 1w9t: Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose

The structure of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose, PDB code: 1w9t 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 / 1.62
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	30.711, 40.967, 56.039, 108.89, 105.87, 90.03
R / Rfree (%)	11.8 / 17.9

The binding sites of Sodium atom in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose (pdb code 1w9t). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 6 binding sites of Sodium where determined in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose, PDB code: 1w9t:
Jump to Sodium binding site number: 1; 2; 3; 4; 5; 6;

Sodium binding site 1 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose


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 Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1141 b:14.8 occ:1.00 O A:ASP38 2.3 15.0 1.0 OD1 A:ASN134 2.4 14.2 1.0 OE1 A:GLN16 2.4 15.0 1.0 O A:ASN134 2.5 14.1 1.0 OE1 A:GLU18 2.5 13.4 1.0 O A:HOH2034 2.5 18.1 1.0 C A:ASN134 3.4 12.8 1.0 CD A:GLU18 3.4 15.9 1.0 C A:ASP38 3.5 15.6 1.0 CG A:ASN134 3.5 14.8 1.0 OE2 A:GLU18 3.6 15.7 1.0 CD A:GLN16 3.6 13.1 1.0 CA A:ASN134 3.7 13.2 1.0 CB A:GLN16 3.9 12.8 1.0 O A:HOH2029 4.0 25.4 1.0 N A:ASP38 4.0 17.0 1.0 CG A:GLN16 4.2 13.0 1.0 N A:ALA17 4.2 11.3 1.0 CB A:ASN134 4.2 14.2 1.0 CA A:GLN16 4.3 12.7 1.0 CA A:ASP38 4.3 16.3 1.0 N A:ASN39 4.5 13.7 1.0 N A:TRP135 4.5 12.3 1.0 CA A:ASN39 4.6 13.9 1.0 ND2 A:ASN134 4.6 14.7 1.0 C A:GLN16 4.6 12.1 1.0 O A:HOH2028 4.6 23.5 1.0 NE2 A:GLN16 4.7 16.2 1.0 CB A:TRP135 4.8 10.9 1.0 CG A:GLU18 4.8 16.6 1.0 N A:GLU18 4.8 13.3 1.0 CD1 A:TRP135 4.9 14.2 1.0 CB A:ASP38 4.9 17.6 1.0 CA A:TRP135 4.9 10.8 1.0

Sodium binding site 2 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose


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 Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1142 b:14.6 occ:1.00 OD2 A:ASP47 2.3 14.2 1.0 O A:TRP42 2.3 13.6 1.0 O A:GLY25 2.3 11.9 1.0 O B:THR84 2.3 13.1 1.0 OD1 A:ASN44 2.4 13.8 1.0 C A:GLY25 3.3 12.7 1.0 C B:THR84 3.4 14.0 1.0 CG A:ASN44 3.4 13.4 1.0 C A:TRP42 3.4 12.8 1.0 CG A:ASP47 3.4 13.8 1.0 N A:ASN44 3.5 13.1 1.0 CB B:THR84 3.6 14.8 1.0 CB A:ASN44 3.7 13.0 1.0 CA B:THR84 3.8 14.1 1.0 O A:HOH2077 3.8 20.0 1.0 CA A:GLY25 3.9 11.6 1.0 OD1 A:ASP47 3.9 13.0 1.0 CA A:ILE43 4.0 13.1 1.0 C A:ILE43 4.0 13.7 1.0 NH1 B:ARG79 4.0 13.3 1.0 N A:ILE43 4.1 13.0 1.0 CA A:ASN44 4.2 13.2 1.0 N A:ILE26 4.4 12.5 1.0 OG1 B:THR84 4.5 15.2 1.0 N B:GLY85 4.5 13.2 1.0 CA A:TRP42 4.6 13.4 1.0 CA A:ILE26 4.6 13.2 1.0 ND2 A:ASN44 4.6 15.6 1.0 CG2 B:THR84 4.6 15.3 1.0 CB A:ASP47 4.6 12.8 1.0 CB A:TRP42 4.6 14.6 1.0 O B:GLY85 4.7 11.9 1.0 CG2 A:ILE26 4.7 14.1 1.0 C B:GLY85 4.8 12.5 1.0 O A:ILE43 4.8 11.6 1.0 O A:HOH2086 4.9 13.3 1.0 CA B:GLY85 4.9 13.3 1.0

Sodium binding site 3 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1143 b:28.1 occ:1.00 O A:HOH2124 2.2 25.6 1.0 OD2 A:ASP90 2.3 22.6 1.0 O A:HOH2150 2.3 17.5 1.0 O A:ASP90 2.3 15.8 1.0 O A:HOH2149 2.7 19.5 1.0 C A:ASP90 3.1 16.3 1.0 CG A:ASP90 3.4 24.3 1.0 N A:ASP90 3.7 15.8 1.0 CA A:ASP90 3.8 16.9 1.0 N A:VAL91 4.1 15.9 1.0 O A:HOH2126 4.1 37.1 1.0 CB A:ASP90 4.2 18.0 1.0 O A:HOH2147 4.2 30.9 1.0 CA A:GLY107 4.3 14.8 1.0 N A:ASN108 4.3 15.8 1.0 OD1 A:ASP90 4.3 31.3 1.0 CA A:VAL91 4.4 17.3 1.0 O A:HOH2146 4.4 17.6 1.0 O A:HOH2123 4.4 43.8 1.0 O A:ASN108 4.5 16.1 1.0 C A:GLY107 4.7 15.7 1.0 O A:HOH2125 4.8 47.0 1.0 C A:GLY89 5.0 14.2 1.0

Sodium binding site 4 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1141 b:14.1 occ:1.00 O B:ASP38 2.3 15.5 1.0 OE1 B:GLN16 2.4 16.4 1.0 OD1 B:ASN134 2.4 14.9 1.0 OE1 B:GLU18 2.5 13.6 1.0 O B:ASN134 2.5 12.7 1.0 O B:HOH2033 2.6 18.9 1.0 CD B:GLU18 3.4 16.2 1.0 C B:ASN134 3.4 12.1 1.0 C B:ASP38 3.5 15.7 1.0 OE2 B:GLU18 3.5 17.3 1.0 CD B:GLN16 3.6 14.1 1.0 CG B:ASN134 3.6 14.7 1.0 CA B:ASN134 3.8 12.2 1.0 CB B:GLN16 3.9 14.7 1.0 O B:HOH2032 3.9 30.3 1.0 N B:ASP38 4.1 16.8 1.0 CG B:GLN16 4.2 14.6 1.0 N B:ALA17 4.2 12.1 1.0 CA B:GLN16 4.2 13.0 1.0 CA B:ASP38 4.3 16.6 1.0 CB B:ASN134 4.3 12.7 1.0 N B:ASN39 4.4 14.8 1.0 N B:TRP135 4.5 12.8 1.0 CA B:ASN39 4.6 13.9 1.0 C B:GLN16 4.6 13.1 1.0 O B:HOH2031 4.6 28.0 1.0 NE2 B:GLN16 4.6 15.9 1.0 ND2 B:ASN134 4.7 14.7 1.0 CB B:TRP135 4.8 13.3 1.0 N B:GLU18 4.8 13.5 1.0 CG B:GLU18 4.8 15.8 1.0 CD1 B:TRP135 4.9 14.9 1.0 CB B:ASP38 4.9 17.0 1.0 CA B:TRP135 4.9 11.7 1.0

Sodium binding site 5 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1142 b:15.2 occ:1.00 OD2 B:ASP47 2.2 13.3 1.0 O B:TRP42 2.3 12.8 1.0 O B:GLY25 2.4 12.1 1.0 OD1 B:ASN44 2.4 12.0 1.0 C B:GLY25 3.3 12.9 1.0 CG B:ASN44 3.3 13.2 1.0 CG B:ASP47 3.4 13.0 1.0 C B:TRP42 3.4 13.2 1.0 N B:ASN44 3.5 13.5 1.0 CB B:ASN44 3.7 13.6 1.0 OD1 B:ASP47 3.9 11.7 1.0 CA B:GLY25 3.9 12.2 1.0 C B:ILE43 3.9 12.7 1.0 CA B:ILE43 4.0 13.0 1.0 N B:ILE43 4.0 12.6 1.0 CA B:ASN44 4.2 13.0 1.0 N B:ILE26 4.4 12.0 1.0 ND2 B:ASN44 4.6 14.0 1.0 CA B:TRP42 4.6 13.2 1.0 CB B:ASP47 4.6 10.8 1.0 CA B:ILE26 4.6 13.2 1.0 CG2 B:ILE26 4.7 13.2 1.0 CB B:TRP42 4.7 14.8 1.0 O B:ILE43 4.8 12.1 1.0 O B:HOH2089 4.9 14.0 1.0

Sodium binding site 6 out of 6 in the Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 6 of Structure of A Beta-1,3-Glucan Binding CBM6 From Bacillus Halodurans in Complex with Xylobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1143 b:28.4 occ:1.00 O B:HOH2127 2.2 26.0 1.0 O B:HOH2150 2.3 20.9 1.0 OD2 B:ASP90 2.3 21.9 1.0 O B:ASP90 2.5 15.2 1.0 C B:ASP90 3.3 15.8 1.0 CG B:ASP90 3.5 23.3 1.0 N B:ASP90 3.8 15.8 1.0 CA B:ASP90 3.9 16.7 1.0 O B:HOH2129 4.2 34.0 1.0 N B:VAL91 4.2 16.0 1.0 CB B:ASP90 4.3 16.6 1.0 CA B:GLY107 4.3 15.8 1.0 N B:ASN108 4.3 16.8 1.0 OD1 B:ASP90 4.3 32.1 1.0 O B:ASN108 4.4 16.4 1.0 O B:HOH2148 4.4 33.3 1.0 O B:HOH2147 4.5 17.1 1.0 CA B:VAL91 4.6 15.9 1.0 C B:GLY107 4.7 16.3 1.0 O B:HOH2085 4.8 39.6 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