Sodium in PDB 4b1m: Carbohydrate Binding Module CBM66 From Bacillus Subtilis

All present enzymatic activity of Carbohydrate Binding Module CBM66 From Bacillus Subtilis:
3.2.1.80;

The structure of Carbohydrate Binding Module CBM66 From Bacillus Subtilis, PDB code: 4b1m was solved by F.Cuskin, J.E.Flint, C.Morland, A.Basle, B.Henrissat, P.M.Countinho, A.Strazzulli, A.Solzehinkin, G.J.Davies, H.J.Gilbert, T.M.Gloster, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	87.35 / 1.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	66.897, 36.909, 87.355, 90.00, 90.61, 90.00
R / Rfree (%)	15.635 / 18.121

The binding sites of Sodium atom in the Carbohydrate Binding Module CBM66 From Bacillus Subtilis (pdb code 4b1m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Carbohydrate Binding Module CBM66 From Bacillus Subtilis, PDB code: 4b1m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Carbohydrate Binding Module CBM66 From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Carbohydrate Binding Module CBM66 From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1680 b:9.6 occ:1.00 O A:ILE620 2.3 8.2 1.0 O A:ALA595 2.4 9.2 1.0 O A:HOH2131 2.4 18.9 1.0 OD1 A:ASP598 2.4 9.3 1.0 O A:HOH2107 2.4 12.7 1.0 O A:HOH2108 2.4 19.7 1.0 C A:ALA595 3.4 7.8 1.0 CG A:ASP598 3.4 9.7 1.0 C A:ILE620 3.5 8.0 1.0 OD2 A:ASP598 3.7 14.8 1.0 O A:HOH2059 3.7 26.7 1.0 CA A:ALA595 3.8 7.1 1.0 N A:ILE620 4.0 8.1 1.0 CB A:ALA595 4.1 8.5 1.0 O A:HOH2058 4.2 26.9 1.0 CA A:ILE620 4.3 7.8 1.0 N A:ASP621 4.5 8.4 1.0 O A:HOH2090 4.5 12.7 1.0 N A:LYS596 4.6 7.8 1.0 O A:HOH2110 4.6 25.4 1.0 O A:HOH2132 4.6 11.1 1.0 CA A:ASP621 4.6 8.9 1.0 CB A:ASP598 4.7 8.2 1.0 OD1 A:ASP621 4.8 12.7 1.0 N A:ASP598 4.9 8.0 1.0 CA A:ASP598 4.9 8.3 1.0 CB A:ILE620 4.9 7.5 1.0 CA A:LYS596 5.0 7.8 1.0 C A:PRO619 5.0 8.5 1.0

Sodium binding site 2 out of 4 in the Carbohydrate Binding Module CBM66 From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Carbohydrate Binding Module CBM66 From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1681 b:21.3 occ:1.00 O A:HOH2015 2.2 21.0 1.0 O A:HOH2011 2.4 14.8 1.0 O A:SER520 2.4 12.1 1.0 O A:HOH2014 2.6 23.6 1.0 O A:HOH2012 2.6 10.2 1.0 C A:SER520 3.6 7.9 1.0 O A:HOH2013 3.7 17.1 1.0 N A:SER520 3.9 8.0 1.0 O A:HOH2017 4.1 21.7 1.0 O A:HOH2009 4.2 15.5 1.0 CA A:SER520 4.2 8.2 1.0 CB A:SER520 4.5 8.7 1.0 O A:PHE518 4.6 9.5 1.0 N A:ASN521 4.6 7.8 1.0 O A:HOH2018 4.6 15.8 1.0 CA A:ASN521 4.8 8.2 1.0 O A:MET522 4.9 10.6 1.0 C A:MET519 4.9 8.2 1.0

Sodium binding site 3 out of 4 in the Carbohydrate Binding Module CBM66 From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Carbohydrate Binding Module CBM66 From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1680 b:14.2 occ:1.00 O B:ILE620 2.3 11.0 1.0 O B:ALA595 2.4 14.1 1.0 OD1 B:ASP598 2.4 13.0 1.0 O B:HOH2084 2.4 23.0 1.0 O B:HOH2090 2.5 22.5 1.0 O B:HOH2085 2.5 31.8 1.0 C B:ALA595 3.4 9.8 1.0 CG B:ASP598 3.4 13.9 1.0 C B:ILE620 3.4 9.9 1.0 CA B:ALA595 3.8 9.3 1.0 OD2 B:ASP598 3.9 21.2 1.0 O B:HOH2089 4.0 27.3 1.0 N B:ILE620 4.1 9.7 1.0 CB B:ALA595 4.2 10.2 1.0 CA B:ILE620 4.3 9.6 1.0 N B:ASP621 4.3 10.6 1.0 O B:HOH2103 4.4 24.6 1.0 CA B:ASP621 4.4 11.5 1.0 O B:HOH2070 4.5 19.1 1.0 N B:LYS596 4.6 10.0 1.0 CB B:ASP598 4.6 11.0 1.0 N B:ASP598 4.6 9.4 1.0 OD1 B:ASP621 4.6 19.9 1.0 CA B:ASP598 4.7 9.5 1.0 CB B:ILE620 4.7 9.2 1.0 C B:LYS596 5.0 10.2 1.0

Sodium binding site 4 out of 4 in the Carbohydrate Binding Module CBM66 From Bacillus Subtilis


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Carbohydrate Binding Module CBM66 From Bacillus Subtilis within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1680 b:11.3 occ:1.00 O C:ILE620 2.3 9.0 1.0 O C:ALA595 2.4 10.3 1.0 OD1 C:ASP598 2.4 9.8 1.0 O C:HOH2089 2.4 16.2 1.0 O C:HOH2096 2.5 18.3 1.0 O C:HOH2088 2.5 19.8 1.0 CG C:ASP598 3.3 10.7 1.0 C C:ALA595 3.4 8.2 1.0 C C:ILE620 3.5 8.3 1.0 OD2 C:ASP598 3.5 17.2 1.0 CA C:ALA595 3.8 8.0 1.0 O C:HOH2097 4.0 23.0 1.0 N C:ILE620 4.0 8.0 1.0 CB C:ALA595 4.2 9.6 1.0 CA C:ILE620 4.3 8.4 1.0 N C:ASP621 4.4 8.7 1.0 O C:HOH2071 4.4 14.7 1.0 O C:HOH2119 4.4 16.4 1.0 CA C:ASP621 4.5 8.9 1.0 N C:LYS596 4.5 8.5 1.0 OD1 C:ASP621 4.6 16.7 1.0 CB C:ASP598 4.6 8.7 1.0 N C:ASP598 4.8 7.4 1.0 CB C:ILE620 4.8 8.8 1.0 CA C:ASP598 4.8 7.7 1.0 CA C:LYS596 5.0 8.7 1.0

F.Cuskin, J.E.Flint, T.M.Gloster, C.Morland, A.Basle, B.Henrissat, P.M.Coutinho, A.Strazzulli, A.S.Solovyova, G.J.Davies, H.J.Gilbert. How Nature Can Exploit Nonspecific Catalytic and Carbohydrate Binding Modules to Create Enzymatic Specificity Proc.Natl.Acad.Sci.Usa V. 109 20889 2012.
ISSN: ISSN 0027-8424
PubMed: 23213210
DOI: 10.1073/PNAS.1212034109