Magnesium in PDB 4zo7: Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose

The structure of Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose, PDB code: 4zo7 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)	32.51 / 2.00
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.600, 95.160, 215.404, 90.00, 96.38, 90.00
R / Rfree (%)	16.3 / 23.5

The binding sites of Magnesium atom in the Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose (pdb code 4zo7). 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 Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose, PDB code: 4zo7:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose


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 Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg803 b:12.6 occ:1.00 O A:HOH1176 2.0 8.9 1.0 O A:HOH1079 2.0 4.3 1.0 O A:THR650 2.1 13.4 1.0 OD1 A:ASP648 2.1 11.4 1.0 O A:HOH995 2.1 8.5 1.0 O A:HOH1070 2.1 12.4 1.0 CG A:ASP648 3.2 13.1 1.0 C A:THR650 3.3 12.8 1.0 OD2 A:ASP648 3.6 13.6 1.0 N A:THR650 3.9 12.1 1.0 CA A:THR650 4.1 13.1 1.0 O A:PRO698 4.2 10.9 1.0 N A:ALA651 4.2 13.8 1.0 O A:HOH1241 4.2 13.5 1.0 CA A:ALA651 4.3 13.3 1.0 O A:LEU700 4.3 10.8 1.0 CB A:ALA651 4.3 14.1 1.0 CA A:GLY699 4.4 12.7 1.0 CB A:ASP648 4.5 13.1 1.0 OE1 A:GLU697 4.6 10.4 1.0 CB A:THR650 4.6 13.1 1.0 O A:GLU697 4.6 11.8 1.0 N A:LEU700 4.6 12.7 1.0 NE2 A:HIS701 4.6 14.0 1.0 C A:GLY699 4.7 12.7 1.0 O B:HOH1280 4.7 22.6 1.0 N A:VAL649 4.7 10.0 1.0 C A:PRO698 4.8 12.7 1.0 CB A:GLU697 4.8 13.9 1.0 C A:ASP648 4.8 12.3 1.0 N A:GLY699 4.8 12.0 1.0 CA A:ASP648 4.8 12.5 1.0 O A:HOH1023 5.0 16.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose


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 Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Gentiobiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:13.2 occ:1.00 O B:HOH925 2.0 9.8 1.0 OD1 B:ASP648 2.0 11.2 1.0 O B:HOH1058 2.0 15.2 1.0 O B:THR650 2.1 14.5 1.0 O B:HOH1148 2.1 12.0 1.0 O B:HOH1049 2.1 15.1 1.0 CG B:ASP648 3.1 12.2 1.0 C B:THR650 3.2 13.3 1.0 OD2 B:ASP648 3.4 12.8 1.0 N B:THR650 3.9 11.3 1.0 CA B:THR650 4.1 12.8 1.0 N B:ALA651 4.1 11.1 1.0 CA B:ALA651 4.1 10.9 1.0 O B:PRO698 4.2 10.3 1.0 CB B:ALA651 4.2 10.7 1.0 O B:LEU700 4.2 15.7 1.0 O B:HOH1232 4.4 9.6 1.0 NE2 B:HIS701 4.4 16.0 1.0 CB B:ASP648 4.4 12.5 1.0 CA B:GLY699 4.5 16.0 1.0 OE1 B:GLU697 4.5 15.4 1.0 O B:GLU697 4.6 11.3 1.0 N B:VAL649 4.6 15.4 1.0 C B:ASP648 4.6 13.0 1.0 N B:LEU700 4.6 14.6 1.0 CB B:THR650 4.7 13.2 1.0 CA B:ASP648 4.7 12.2 1.0 C B:GLY699 4.7 16.7 1.0 C B:PRO698 4.8 12.9 1.0 CE1 B:HIS701 4.8 13.2 1.0 O B:HOH1039 4.9 10.8 1.0 CB B:GLU697 4.9 13.9 1.0 CD2 B:HIS701 5.0 13.4 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