Sodium in PDB 2w46: CBM35 From Cellvibrio Japonicus ABF62

All present enzymatic activity of CBM35 From Cellvibrio Japonicus ABF62:
3.2.1.55;

The structure of CBM35 From Cellvibrio Japonicus ABF62, PDB code: 2w46 was solved by C.Montainer, A.Lammerts Van Bueren, C.Dumon, J.E.Flint, M.A.Correia, J.A.Prates, S.J.Firbank, R.J.Lewis, G.G.Grondin, M.G.Ghinet, T.M.Gloster, C.Herve, J.P.Knox, B.G.Talbot, J.P.Turkenburg, J.Kerovuo, R.Brzezinski, C.M.G.A.Fontes, G.J.Davies, A.B.Boraston, H.J.Gilbert, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.88 / 1.90
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	28.216, 46.135, 49.006, 71.61, 89.78, 82.19
R / Rfree (%)	13.7 / 21.8

The structure of CBM35 From Cellvibrio Japonicus ABF62 also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the CBM35 From Cellvibrio Japonicus ABF62 (pdb code 2w46). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the CBM35 From Cellvibrio Japonicus ABF62, PDB code: 2w46:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the CBM35 From Cellvibrio Japonicus ABF62


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of CBM35 From Cellvibrio Japonicus ABF62 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1149 b:6.6 occ:1.00 OD1 A:ASN40 2.2 4.3 1.0 O A:HOH2088 2.3 22.4 1.0 O A:HOH2193 2.3 9.3 1.0 O A:THR41 2.5 4.3 1.0 O A:HOH2197 2.5 5.6 1.0 O A:HOH2195 2.6 11.9 1.0 O A:HOH2081 3.5 34.2 1.0 CG A:ASN40 3.5 6.5 1.0 ND2 A:ASN43 3.6 13.1 1.0 N A:THR41 3.6 5.3 1.0 C A:THR41 3.6 5.8 1.0 OG1 A:THR41 3.9 5.0 1.0 C A:ASN40 3.9 4.7 1.0 NH1 A:ARG75 4.0 7.1 1.0 CA A:THR41 4.1 4.3 1.0 ND2 A:ASN130 4.1 4.3 1.0 O A:LEU128 4.2 4.8 1.0 CA A:ASN40 4.3 5.2 1.0 ND2 A:ASN40 4.3 8.8 1.0 O A:HOH2079 4.4 29.5 1.0 O A:HOH2136 4.5 14.1 1.0 CB A:ASN40 4.5 4.8 1.0 O A:HOH2032 4.5 19.6 1.0 O A:ASN40 4.6 5.5 1.0 CB A:THR41 4.6 4.6 1.0 CG A:ASN43 4.7 14.2 1.0 O A:GLU126 4.7 6.1 1.0 O A:ASN42 4.8 6.4 1.0 C A:ASN42 4.8 6.6 1.0 N A:ASN42 4.8 5.7 1.0 O A:HOH2080 4.8 25.9 1.0

Sodium binding site 2 out of 2 in the CBM35 From Cellvibrio Japonicus ABF62


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of CBM35 From Cellvibrio Japonicus ABF62 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1149 b:7.2 occ:1.00 OD1 B:ASN40 2.3 7.5 1.0 O B:HOH2081 2.3 14.5 1.0 O B:HOH2180 2.3 6.2 1.0 O B:THR41 2.4 2.8 1.0 O B:HOH2182 2.6 7.7 1.0 O B:HOH2183 2.6 15.4 1.0 C B:THR41 3.5 4.0 1.0 CG B:ASN40 3.5 8.6 1.0 N B:THR41 3.6 4.2 1.0 OD1 B:ASN43 3.7 18.5 1.0 OG1 B:THR41 3.8 4.3 1.0 C B:ASN40 3.9 4.9 1.0 CA B:THR41 4.0 3.9 1.0 O B:HOH2070 4.1 16.3 1.0 NH1 B:ARG75 4.1 5.9 1.0 OD1 B:ASN130 4.1 5.8 1.0 O B:LEU128 4.2 6.0 1.0 CA B:ASN40 4.2 5.4 1.0 ND2 B:ASN40 4.4 10.5 1.0 CB B:ASN40 4.5 5.3 1.0 O B:ASN40 4.5 4.0 1.0 O B:HOH2068 4.5 41.1 1.0 O B:HOH2121 4.6 15.9 1.0 CB B:THR41 4.6 4.5 1.0 O B:HOH2025 4.6 20.7 1.0 N B:ASN42 4.6 3.7 1.0 O B:ASN42 4.7 5.1 1.0 C B:ASN42 4.7 5.0 1.0 O B:GLU126 4.8 7.6 1.0 CG B:ASN43 4.8 12.9 1.0

C.Montanier, A.L.Van Bueren, C.Dumon, J.E.Flint, M.A.Correia, J.A.Prates, S.J.Firbank, R.J.Lewis, G.G.Grondin, M.G.Ghinet, T.M.Gloster, C.Herve, J.P.Knox, B.G.Talbot, J.P.Turkenburg, J.Kerovuo, R.Brzezinski, C.M.G.A.Fontes, G.J.Davies, A.B.Boraston, H.J.Gilbert. Evidence That Family 35 Carbohydrate Binding Modules Display Conserved Specificity But Divergent Function. Proc.Natl.Acad.Sci.Usa V. 106 3065 2009.
ISSN: ISSN 0027-8424
PubMed: 19218457
DOI: 10.1073/PNAS.0808972106