Magnesium in PDB 4zod: Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Glucose

The structure of Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Glucose, PDB code: 4zod was solved by M.Nakajima, R.Yoshida, A.Miyanaga, K.Abe, Y.Takahashi, N.Sugimoto, H.Toyoizumi, H.Nakai, M.Kitaoka, H.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	37.10 / 2.10
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.790, 95.410, 213.233, 90.00, 97.27, 90.00
R / Rfree (%)	16.7 / 23.3

The binding sites of Magnesium atom in the Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Glucose (pdb code 4zod). 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 Beta-Glucosidase From Listeria Innocua in Complex with Glucose, PDB code: 4zod:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Glucose


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 Beta-Glucosidase From Listeria Innocua in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:24.2 occ:1.00 O A:HOH994 1.9 22.7 1.0 O A:THR650 2.0 21.5 1.0 O A:HOH989 2.0 16.3 1.0 OD1 A:ASP648 2.1 22.2 1.0 O A:HOH956 2.1 18.2 1.0 O A:HOH1072 2.1 15.0 1.0 CG A:ASP648 3.1 20.2 1.0 C A:THR650 3.1 22.0 1.0 OD2 A:ASP648 3.3 14.6 1.0 CA A:ALA651 4.0 20.1 1.0 N A:ALA651 4.0 21.6 1.0 CB A:ALA651 4.1 21.6 1.0 N A:THR650 4.1 22.8 1.0 CA A:THR650 4.1 20.9 1.0 O A:PRO698 4.3 18.4 1.0 O A:HOH1090 4.3 19.4 1.0 OE1 A:GLU697 4.4 22.4 1.0 O A:LEU700 4.4 20.7 1.0 CA A:GLY699 4.4 21.3 1.0 CB A:ASP648 4.5 23.5 1.0 NE2 A:HIS701 4.5 24.8 1.0 O A:GLU697 4.5 21.6 1.0 CB A:GLU697 4.6 23.2 1.0 O A:HOH1069 4.6 25.2 1.0 CB A:THR650 4.7 20.7 1.0 C A:GLY699 4.8 22.0 1.0 N A:LEU700 4.8 22.3 1.0 N A:VAL649 4.8 21.2 1.0 C A:ASP648 4.8 23.6 1.0 CA A:ASP648 4.8 22.1 1.0 C A:PRO698 4.9 19.5 1.0 N A:GLY699 5.0 20.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Glucose


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 Beta-Glucosidase From Listeria Innocua in Complex with Glucose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg804 b:24.1 occ:1.00 O B:THR650 1.8 21.3 1.0 O B:HOH947 1.9 24.2 1.0 OD1 B:ASP648 1.9 24.8 1.0 O B:HOH990 2.0 20.6 1.0 O B:HOH1028 2.1 18.0 1.0 O B:HOH1091 2.2 17.1 1.0 C B:THR650 3.0 23.9 1.0 CG B:ASP648 3.0 20.6 1.0 OD2 B:ASP648 3.4 17.0 1.0 N B:THR650 3.7 23.6 1.0 CA B:THR650 3.9 22.6 1.0 N B:ALA651 3.9 21.1 1.0 CA B:ALA651 4.0 19.4 1.0 CB B:ALA651 4.1 21.4 1.0 O B:LEU700 4.3 26.0 1.0 CB B:ASP648 4.3 22.7 1.0 O A:HOH1108 4.4 17.3 1.0 O B:PRO698 4.4 24.1 1.0 N B:VAL649 4.5 21.4 1.0 OE1 B:GLU697 4.5 28.8 1.0 CB B:THR650 4.5 24.4 1.0 CA B:GLY699 4.5 27.2 1.0 NE2 B:HIS701 4.5 23.7 1.0 C B:ASP648 4.6 23.6 1.0 CA B:ASP648 4.7 21.8 1.0 N B:LEU700 4.7 24.5 1.0 O B:HOH1087 4.7 29.9 1.0 O B:GLU697 4.7 22.7 1.0 C B:GLY699 4.8 27.0 1.0 C B:VAL649 4.9 22.8 1.0 O B:HOH1053 4.9 22.7 1.0 CB B:GLU697 5.0 25.8 1.0

M.Nakajima, R.Yoshida, A.Miyanaga, K.Abe, Y.Takahashi, N.Sugimoto, H.Toyoizumi, H.Nakai, M.Kitaoka, H.Taguchi. Functional and Structural Analysis of A Beta-Glucosidase Involved in Beta-1,2-Glucan Metabolism in Listeria Innocua Plos One V. 11 48870 2016.
ISSN: ESSN 1932-6203
PubMed: 26886583
DOI: 10.1371/JOURNAL.PONE.0148870