Magnesium in PDB 4zo9: Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Laminaribiose

The structure of Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Laminaribiose, PDB code: 4zo9 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)	36.91 / 1.99
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.490, 94.760, 215.232, 90.00, 96.32, 90.00
R / Rfree (%)	18.9 / 25.7

The binding sites of Magnesium atom in the Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Laminaribiose (pdb code 4zo9). 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 Laminaribiose, PDB code: 4zo9:
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 Laminaribiose


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 Laminaribiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:13.9 occ:1.00 O A:HOH1033 1.9 16.8 1.0 OD1 A:ASP648 1.9 12.4 1.0 O A:HOH1133 1.9 8.2 1.0 O A:THR650 2.3 11.3 1.0 O A:HOH993 2.3 11.7 1.0 O A:HOH1032 2.3 27.6 1.0 CG A:ASP648 2.9 10.6 1.0 OD2 A:ASP648 3.2 9.7 1.0 C A:THR650 3.5 12.7 1.0 CB A:ALA651 4.1 14.1 1.0 O A:PRO698 4.1 13.8 1.0 CA A:ALA651 4.1 14.5 1.0 N A:THR650 4.2 10.2 1.0 N A:ALA651 4.3 15.7 1.0 CB A:ASP648 4.3 10.3 1.0 O A:GLU697 4.3 12.0 1.0 NE2 A:HIS701 4.3 10.7 1.0 O A:LEU700 4.4 12.6 1.0 OE1 A:GLU697 4.4 12.1 1.0 CA A:THR650 4.4 11.9 1.0 O A:HOH1013 4.4 12.4 1.0 CB A:GLU697 4.5 14.3 1.0 O A:HOH1051 4.6 17.0 1.0 CA A:GLY699 4.7 13.4 1.0 CE1 A:HIS701 4.7 10.9 1.0 CA A:ASP648 4.7 10.3 1.0 C A:PRO698 4.7 15.9 1.0 N A:LEU700 4.8 13.2 1.0 C A:ASP648 4.8 10.1 1.0 N A:VAL649 4.8 11.3 1.0 C A:GLY699 4.8 15.2 1.0 CB A:THR650 4.9 12.0 1.0 C A:GLU697 5.0 14.9 1.0 CD2 A:HIS701 5.0 12.6 1.0 O A:HOH1190 5.0 20.8 1.0

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


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 Laminaribiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:18.1 occ:1.00 OD1 B:ASP648 2.0 13.7 1.0 O B:HOH1085 2.1 10.7 1.0 O B:THR650 2.1 18.6 1.0 O B:HOH921 2.1 15.4 1.0 O B:HOH930 2.2 15.0 1.0 O B:HOH949 2.3 11.4 1.0 CG B:ASP648 2.9 12.0 1.0 OD2 B:ASP648 3.2 11.0 1.0 C B:THR650 3.3 14.8 1.0 N B:THR650 4.0 11.1 1.0 CB B:ALA651 4.1 9.8 1.0 CA B:ALA651 4.1 10.5 1.0 CA B:THR650 4.1 15.1 1.0 N B:ALA651 4.1 12.2 1.0 O B:LEU700 4.2 11.1 1.0 O B:PRO698 4.3 11.1 1.0 CB B:ASP648 4.3 13.5 1.0 O B:HOH1122 4.4 13.8 1.0 NE2 B:HIS701 4.4 13.3 1.0 N B:VAL649 4.5 13.6 1.0 C B:ASP648 4.5 13.2 1.0 O B:GLU697 4.6 12.9 1.0 OE1 B:GLU697 4.6 12.0 1.0 CA B:GLY699 4.6 13.9 1.0 CB B:THR650 4.6 15.5 1.0 CA B:ASP648 4.7 12.5 1.0 CB B:GLU697 4.8 16.7 1.0 C B:GLY699 4.8 13.3 1.0 N B:LEU700 4.8 12.8 1.0 CD2 B:HIS701 4.9 11.9 1.0 O B:HOH1015 4.9 12.5 1.0 C B:PRO698 4.9 14.8 1.0 CE1 B:HIS701 4.9 11.6 1.0 O B:ASP648 5.0 16.0 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