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

The structure of Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Gluconolactone, PDB code: 4zob 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)	41.91 / 2.40
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	90.360, 95.810, 213.310, 90.00, 97.20, 90.00
R / Rfree (%)	17 / 25

The binding sites of Magnesium atom in the Crystal Structure of Beta-Glucosidase From Listeria Innocua in Complex with Gluconolactone (pdb code 4zob). 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 Gluconolactone, PDB code: 4zob:
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 Gluconolactone


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 Gluconolactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:28.3 occ:1.00 O A:HOH928 1.7 24.9 1.0 O A:THR650 2.0 16.0 1.0 OD1 A:ASP648 2.0 21.2 1.0 O A:HOH1017 2.1 34.1 1.0 O A:HOH955 2.3 18.9 1.0 CG A:ASP648 2.9 22.4 1.0 OD2 A:ASP648 3.1 19.9 1.0 C A:THR650 3.2 18.3 1.0 CB A:ALA651 3.9 18.6 1.0 CA A:ALA651 4.0 18.0 1.0 N A:ALA651 4.0 17.9 1.0 N A:THR650 4.1 21.8 1.0 CA A:THR650 4.2 20.2 1.0 CB A:ASP648 4.4 23.4 1.0 O A:LEU700 4.4 19.6 1.0 OE1 A:GLU697 4.4 20.8 1.0 O A:PRO698 4.4 25.1 1.0 CA A:GLY699 4.5 20.9 1.0 CB A:GLU697 4.5 22.9 1.0 O A:GLU697 4.5 25.7 1.0 NE2 A:HIS701 4.6 28.0 1.0 O A:HOH1075 4.7 17.6 1.0 N A:VAL649 4.7 23.6 1.0 N A:LEU700 4.7 21.0 1.0 C A:ASP648 4.7 20.7 1.0 CB A:THR650 4.8 21.5 1.0 CA A:ASP648 4.8 23.4 1.0 C A:GLY699 4.8 21.9 1.0 O A:HOH1011 4.9 22.0 1.0 C A:PRO698 4.9 22.9 1.0 N A:GLY699 5.0 21.0 1.0

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


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 Gluconolactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg805 b:26.0 occ:1.00 O B:THR650 1.8 19.4 1.0 O B:HOH969 1.9 17.4 1.0 O B:HOH942 1.9 18.2 1.0 O B:HOH966 2.0 16.3 1.0 OD1 B:ASP648 2.0 21.1 1.0 O B:HOH994 2.1 25.6 1.0 C B:THR650 3.0 20.5 1.0 CG B:ASP648 3.1 22.7 1.0 OD2 B:ASP648 3.4 21.1 1.0 N B:THR650 3.8 25.5 1.0 CA B:THR650 3.9 21.5 1.0 N B:ALA651 4.0 19.9 1.0 CA B:ALA651 4.1 20.2 1.0 CB B:ALA651 4.1 19.1 1.0 O B:LEU700 4.2 26.1 1.0 O B:HOH1061 4.2 16.3 1.0 CA B:GLY699 4.3 28.7 1.0 O B:PRO698 4.3 25.2 1.0 CB B:ASP648 4.4 24.1 1.0 CB B:THR650 4.4 19.4 1.0 N B:LEU700 4.5 30.2 1.0 NE2 B:HIS701 4.5 33.4 1.0 O B:GLU697 4.6 24.0 1.0 C B:GLY699 4.6 29.6 1.0 OE1 B:GLU697 4.7 20.9 1.0 C B:ASP648 4.7 24.2 1.0 CB B:GLU697 4.7 23.4 1.0 N B:VAL649 4.7 22.2 1.0 CA B:ASP648 4.8 24.5 1.0 O B:HOH1003 4.8 19.6 1.0 C B:PRO698 4.8 25.8 1.0 N B:GLY699 4.9 26.0 1.0 CD2 B:HIS701 5.0 29.7 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