Sodium in PDB 6fwq: Structure of An E333Q Variant of the GH99 Endo-Alpha-Mannanase From Bacteroides Xylanisolvens in Complex with Alpha-1,3-Mannobiose and Alpha-1,2-Mannobiose

The structure of Structure of An E333Q Variant of the GH99 Endo-Alpha-Mannanase From Bacteroides Xylanisolvens in Complex with Alpha-1,3-Mannobiose and Alpha-1,2-Mannobiose, PDB code: 6fwq was solved by L.F.Sobala, G.Speciale, Z.Hakki, P.Z.Fernandes, L.Raich, V.Rojas-Cervellera, A.Bennet, A.J.Thompson, G.Bernardo-Seisdedos, O.Millet, S.Zhu, D.Lu, M.Sollogoub, C.Rovira, J.Jimenez-Barbero, G.J.Davies, S.J.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	76.83 / 1.65
Space group	I 4
Cell size a, b, c (Å), α, β, γ (°)	108.651, 108.651, 68.813, 90.00, 90.00, 90.00
R / Rfree (%)	14.6 / 18.9

The binding sites of Sodium atom in the Structure of An E333Q Variant of the GH99 Endo-Alpha-Mannanase From Bacteroides Xylanisolvens in Complex with Alpha-1,3-Mannobiose and Alpha-1,2-Mannobiose (pdb code 6fwq). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Structure of An E333Q Variant of the GH99 Endo-Alpha-Mannanase From Bacteroides Xylanisolvens in Complex with Alpha-1,3-Mannobiose and Alpha-1,2-Mannobiose, PDB code: 6fwq:

Sodium binding site 1 out of 1 in the Structure of An E333Q Variant of the GH99 Endo-Alpha-Mannanase From Bacteroides Xylanisolvens in Complex with Alpha-1,3-Mannobiose and Alpha-1,2-Mannobiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of An E333Q Variant of the GH99 Endo-Alpha-Mannanase From Bacteroides Xylanisolvens in Complex with Alpha-1,3-Mannobiose and Alpha-1,2-Mannobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na400 b:36.5 occ:1.00 OD1 A:ASP40 2.4 28.5 1.0 OH A:TYR184 2.4 28.0 1.0 O A:TYR39 2.4 27.5 1.0 O A:HOH651 2.5 50.4 1.0 C A:TYR39 3.4 26.6 1.0 CG A:ASP40 3.5 30.4 1.0 CZ A:TYR184 3.6 25.8 1.0 CA A:ASP40 3.7 26.5 1.0 N A:ASP40 3.8 24.6 1.0 CE1 A:TYR184 4.0 26.8 1.0 CB A:ASP40 4.1 29.4 1.0 CG A:LYS186 4.4 46.2 1.0 CZ A:PHE42 4.4 23.5 1.0 OD2 A:ASP40 4.5 33.0 1.0 CA A:TYR39 4.6 26.6 1.0 CB A:TYR39 4.6 26.8 1.0 CE1 A:PHE42 4.7 23.0 1.0 CE2 A:TYR184 4.8 29.4 1.0 CB A:LYS186 4.9 42.2 1.0

L.F.Sobala, G.Speciale, Z.Hakki, P.Z.Fernandes, L.Raich, V.Rojas-Cervellera, A.Bennet, A.J.Thompson, G.Bernardo-Seisdedos, O.Millet, S.Zhu, D.Lu, M.Sollogoub, C.Rovira, J.Jimenez-Barbero, G.J.Davies, S.J.Williams. An Epoxide Intermediate in Glycosidase Catalysis Chemrxiv 2019.
DOI: 10.26434/CHEMRXIV.9745388.V1