Sodium in PDB 8va3: Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome

The structure of Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome, PDB code: 8va3 was solved by M.P.Martins, M.A.B.Morais, M.Chinaglia, F.Mandelli, E.A.Lima, M.T.Murakami, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.07 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	94.055, 105.352, 190.409, 90, 90, 90
R / Rfree (%)	15.5 / 18.7

The structure of Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome also contains other interesting chemical elements:

Magnesium

(Mg)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome (pdb code 8va3). 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 CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome, PDB code: 8va3:

Sodium binding site 1 out of 1 in the Crystal Structure of CAPGH3B 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 CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ A:Na819 b:31.0 occ:1.00 O A:TYR467 2.2 22.3 1.0 O A:PRO465 2.3 26.0 1.0 O A:HOH924 2.3 30.8 1.0 O A:HOH1437 2.3 34.7 1.0 OE1 A:GLU472 2.5 22.0 1.0 CD A:GLU472 3.2 23.1 1.0 OE2 A:GLU472 3.2 30.8 1.0 C A:TYR467 3.4 26.4 1.0 C A:PRO465 3.4 27.1 1.0 C A:GLN466 4.0 25.6 1.0 N A:TYR467 4.0 22.3 1.0 CA A:LYS468 4.2 20.4 1.0 O A:GLN466 4.2 23.9 1.0 N A:LYS468 4.2 22.9 1.0 CA A:PRO465 4.2 24.4 1.0 O A:HOH1519 4.3 34.2 1.0 CA A:TYR467 4.3 23.5 1.0 N A:GLN466 4.3 25.2 1.0 CA A:GLN466 4.4 27.8 1.0 O3 A:GOL812 4.5 31.0 1.0 N A:THR469 4.6 20.9 1.0 CG A:GLU472 4.6 24.2 1.0 CD1 A:LEU444 4.6 21.9 1.0 C A:LYS468 4.8 20.7 1.0 CD A:LYS468 4.8 31.9 1.0 CB A:PRO465 4.9 30.6 1.0 CG2 A:THR469 4.9 22.3 1.0

F.Mandelli, M.P.Martins, M.Chinaglia, E.A.Lima, M.A.B.Morais, T.B.Lima, L.Cabral, R.A.S.Pirolla, F.J.Fuzita, D.A.A.Paixao, M.O.Andrade, L.D.Wolf, P.S.Vieira, G.F.Persinoti, M.T.Murakami. A Functionally Augmented Carbohydrate Utilization Locus From Herbivore Gut Microbiota Fueled By Dietary Beta-Glucans. Npj Biofilms Microbiomes V. 10 105 2024.
ISSN: ISSN 2055-5008
PubMed: 39397008
DOI: 10.1038/S41522-024-00578-6