Sodium in PDB 8d89: Crystal Structure of A Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome

The structure of Crystal Structure of A Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome, PDB code: 8d89 was solved by M.P.Martins, M.A.B.Morais, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.77 / 1.60
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.6, 58.86, 60.66, 90, 90, 90
R / Rfree (%)	17.1 / 19.4

The structure of Crystal Structure of A Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of A Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome (pdb code 8d89). 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 Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome, PDB code: 8d89:

Sodium binding site 1 out of 1 in the Crystal Structure of A Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome


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 Novel GH5 Enzyme Retrieved From Capybara Gut Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na503 b:20.1 occ:1.00 O A:HOH746 2.8 30.4 1.0 OG1 A:THR382 3.0 20.9 1.0 N A:LYS379 3.3 15.8 1.0 CA A:PHE378 3.6 12.6 1.0 CB A:THR382 3.7 19.7 1.0 O A:HOH871 3.8 21.8 1.0 CB A:PHE378 3.8 20.0 1.0 CG2 A:THR382 3.8 27.4 1.0 CG A:LYS379 3.9 18.1 1.0 C A:PHE378 3.9 15.3 1.0 O A:LYS379 4.1 20.2 1.0 CB A:TYR384 4.2 18.9 1.0 CA A:LYS379 4.3 16.8 1.0 N A:GLY385 4.4 17.0 1.0 O A:SER377 4.5 24.6 1.0 CB A:LYS379 4.6 18.4 1.0 C A:LYS379 4.6 17.5 1.0 N A:PHE378 4.8 17.0 1.0 CA A:TYR384 5.0 16.0 1.0

M.P.Martins, M.A.B.Morais, G.F.Persinoti, R.H.Galinari, L.Yu, Y.Yoshimi, F.B.Passos Nunes, T.B.Lima, S.F.Barbieri, J.L.M.Silveira, V.Lombard, N.Terrapon, P.Dupree, B.Henrissat, M.T.Murakami. Glycoside Hydrolase Subfamily GH5_57 Features A Highly Redesigned Catalytic Interface to Process Complex Hetero-Beta-Mannans. Acta Crystallogr D Struct V. 78 1358 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36322419
DOI: 10.1107/S2059798322009561