Sodium in PDB 6uaq: Crystal Structure of A GH128 (Subgroup I) Endo-Beta-1,3-Glucanase From Amycolatopsis Mediterranei (AMGH128_I)

The structure of Crystal Structure of A GH128 (Subgroup I) Endo-Beta-1,3-Glucanase From Amycolatopsis Mediterranei (AMGH128_I), PDB code: 6uaq was solved by P.A.C.R.Costa, C.R.Santos, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.28 / 1.15
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	37.350, 78.643, 46.183, 90.00, 101.62, 90.00
R / Rfree (%)	15 / 16.2

The binding sites of Sodium atom in the Crystal Structure of A GH128 (Subgroup I) Endo-Beta-1,3-Glucanase From Amycolatopsis Mediterranei (AMGH128_I) (pdb code 6uaq). 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 Crystal Structure of A GH128 (Subgroup I) Endo-Beta-1,3-Glucanase From Amycolatopsis Mediterranei (AMGH128_I), PDB code: 6uaq:

Sodium binding site 1 out of 1 in the Crystal Structure of A GH128 (Subgroup I) Endo-Beta-1,3-Glucanase From Amycolatopsis Mediterranei (AMGH128_I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A GH128 (Subgroup I) Endo-Beta-1,3-Glucanase From Amycolatopsis Mediterranei (AMGH128_I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:14.0 occ:1.00 O A:LYS91 2.3 11.3 1.0 O A:GLY94 2.3 11.5 1.0 O A:HOH595 2.4 34.2 1.0 O A:HOH672 2.4 15.6 1.0 O A:HOH629 2.4 22.6 1.0 O A:HOH631 2.6 31.6 1.0 C A:GLY94 3.4 9.3 1.0 C A:LYS91 3.5 9.7 1.0 CG A:LYS91 3.9 10.0 1.0 O A:HOH712 3.9 42.2 1.0 CA A:LYS91 4.1 10.0 1.0 CA A:SER95 4.2 10.0 1.0 O A:HOH640 4.2 40.2 1.0 N A:SER95 4.2 9.4 1.0 N A:GLY94 4.4 11.0 1.0 CA A:GLY94 4.5 10.4 1.0 N A:ALA92 4.5 10.7 1.0 OG A:SER95 4.5 17.8 0.5 O A:HOH665 4.6 23.5 1.0 O A:HOH466 4.6 22.2 1.0 CB A:LYS91 4.6 10.0 1.0 CA A:ALA92 4.7 12.0 1.0 C A:ALA92 4.8 12.2 1.0 CB A:SER95 4.8 12.9 0.5 CE A:MET128 4.9 10.5 1.0 O A:ALA92 4.9 15.9 1.0 CB A:SER95 5.0 13.5 0.5

C.R.Santos, E.A.Lima, F.Mandelli, M.T.Murakami. Structural Insights Into Beta-1,3-Glucan Cleavage By A Glycoside Hydrolase Family Nat.Chem.Biol. 2020.
ISSN: ESSN 1552-4469
DOI: 10.1038/S41589-020-0554-5