Magnesium 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:

Sodium

(Na)

1 atom

The binding sites of Magnesium 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 Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome, PDB code: 8va3:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg 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:Mg818 b:21.1 occ:1.00 O A:ALA705 2.0 24.1 1.0 OD1 A:ASP703 2.0 19.3 1.0 O A:HOH1029 2.1 21.7 1.0 O A:HOH1108 2.1 20.3 1.0 O A:HOH989 2.1 20.6 1.0 O A:HOH1206 2.2 24.6 1.0 CG A:ASP703 3.0 24.6 1.0 C A:ALA705 3.2 24.6 1.0 OD2 A:ASP703 3.3 19.9 1.0 N A:ALA705 3.8 20.8 1.0 CA A:ALA705 4.1 20.0 1.0 O A:ASP755 4.2 19.7 1.0 O1 A:GOL817 4.2 31.1 1.0 N A:ALA706 4.2 23.6 1.0 CA A:ALA706 4.2 21.9 1.0 CB A:ALA706 4.3 20.3 1.0 O A:ALA753 4.4 21.3 1.0 CB A:ASP703 4.4 19.0 1.0 O A:GLU752 4.4 22.5 1.0 N A:LEU704 4.4 20.4 1.0 OE1 A:GLU752 4.5 22.2 1.0 O A:HOH1465 4.5 40.5 1.0 CA A:GLY754 4.5 24.9 1.0 CB A:GLU752 4.6 17.6 1.0 C A:ASP703 4.7 21.5 1.0 C A:GLY754 4.7 30.8 1.0 CZ A:PHE756 4.7 17.3 1.0 N A:ASP755 4.8 22.5 1.0 CA A:ASP703 4.8 19.1 1.0 CB A:ALA705 4.8 23.0 1.0 O A:HOH1402 4.9 22.4 1.0 CE2 A:PHE756 4.9 20.8 1.0 C A:ALA753 5.0 22.1 1.0 C A:LEU704 5.0 23.8 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of CAPGH3B Enzyme Retrieved From Capybara Gut Metagenome within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg814 b:24.2 occ:1.00 O B:ALA705 2.0 21.1 1.0 O B:HOH954 2.0 22.6 1.0 O B:HOH1129 2.1 22.9 1.0 OD1 B:ASP703 2.1 22.6 1.0 O B:HOH1145 2.1 26.9 1.0 O B:HOH1071 2.1 21.9 1.0 CG B:ASP703 3.0 23.1 1.0 C B:ALA705 3.2 20.8 1.0 OD2 B:ASP703 3.3 22.9 1.0 N B:ALA705 3.8 19.9 1.0 CA B:ALA705 4.1 20.3 1.0 N B:ALA706 4.2 21.9 1.0 CA B:ALA706 4.2 23.2 1.0 O B:ASP755 4.2 24.9 1.0 O B:HOH1430 4.3 33.3 1.0 O B:ALA753 4.3 25.4 1.0 CB B:ALA706 4.4 19.4 1.0 O B:HOH1443 4.4 46.0 1.0 OE1 B:GLU752 4.4 25.2 1.0 CB B:ASP703 4.4 19.1 1.0 O B:GLU752 4.4 23.8 1.0 CB B:GLU752 4.5 22.9 1.0 N B:LEU704 4.5 23.5 1.0 CA B:GLY754 4.6 29.6 1.0 C B:ASP703 4.6 21.6 1.0 CB B:ALA705 4.7 22.8 1.0 C B:GLY754 4.8 30.1 1.0 CZ B:PHE756 4.8 21.2 1.0 CA B:ASP703 4.8 21.5 1.0 N B:ASP755 4.9 25.2 1.0 O B:HOH1383 5.0 22.4 1.0 C B:LEU704 5.0 24.0 1.0 C B:ALA753 5.0 29.6 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