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

The structure of Crystal Structure of Mutant (D270A) Beta-Glucosidase From Listeria Innocua in Complex with Sophorotriose, PDB code: 4zoc 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)	32.50 / 1.79
Space group	I 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	89.620, 94.860, 215.065, 90.00, 96.33, 90.00
R / Rfree (%)	14.1 / 19.6

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


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 Sophorotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg802 b:11.4 occ:1.00 OD1 A:ASP648 2.0 10.1 1.0 O A:HOH1291 2.0 8.7 1.0 O A:HOH1007 2.1 11.4 1.0 O A:HOH1081 2.1 8.8 1.0 O A:THR650 2.1 8.9 1.0 O A:HOH1088 2.1 11.2 1.0 CG A:ASP648 3.0 10.2 1.0 C A:THR650 3.3 10.9 1.0 OD2 A:ASP648 3.4 12.8 1.0 N A:THR650 4.1 10.0 1.0 N A:ALA651 4.2 11.9 1.0 CA A:ALA651 4.2 10.9 1.0 CB A:ALA651 4.2 8.3 1.0 O A:HOH1388 4.2 12.8 1.0 CA A:THR650 4.2 10.9 1.0 O A:PRO698 4.2 9.1 1.0 O A:LEU700 4.3 12.8 1.0 O A:HOH1281 4.3 25.4 1.0 NE2 A:HIS701 4.3 12.8 1.0 CB A:ASP648 4.4 9.8 1.0 CA A:GLY699 4.4 10.6 1.0 O A:GLU697 4.5 9.2 1.0 OE1 A:GLU697 4.6 11.7 1.0 N A:VAL649 4.6 9.0 1.0 O A:HOH1544 4.7 30.1 1.0 C A:GLY699 4.7 10.3 1.0 CB A:GLU697 4.7 12.4 1.0 C A:ASP648 4.7 9.4 1.0 O A:HOH1223 4.7 13.3 1.0 CA A:ASP648 4.7 8.0 1.0 N A:LEU700 4.7 10.7 1.0 CB A:THR650 4.7 9.6 1.0 C A:PRO698 4.8 11.0 1.0 CE1 A:HIS701 4.8 10.3 1.0 N A:GLY699 4.8 9.9 1.0 CD2 A:HIS701 4.9 12.0 1.0

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


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 Sophorotriose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg802 b:11.5 occ:1.00 OD1 B:ASP648 2.0 8.7 1.0 O B:HOH950 2.1 10.1 1.0 O B:THR650 2.1 10.7 1.0 O B:HOH1191 2.1 10.3 1.0 O B:HOH970 2.2 8.8 1.0 O B:HOH955 2.2 9.5 1.0 CG B:ASP648 3.0 10.1 1.0 C B:THR650 3.3 11.2 1.0 OD2 B:ASP648 3.4 11.6 1.0 N B:THR650 3.9 11.6 1.0 O B:HOH1232 4.1 19.0 1.0 CA B:THR650 4.2 12.7 1.0 CA B:ALA651 4.2 9.6 1.0 N B:ALA651 4.2 11.2 1.0 O B:LEU700 4.2 12.1 1.0 CB B:ALA651 4.2 9.3 1.0 O B:HOH1268 4.2 9.8 1.0 O B:PRO698 4.2 10.2 1.0 NE2 B:HIS701 4.3 15.8 1.0 CA B:GLY699 4.4 11.0 1.0 CB B:ASP648 4.4 11.2 1.0 OE1 B:GLU697 4.5 9.1 1.0 O B:GLU697 4.5 12.3 1.0 N B:VAL649 4.6 10.8 1.0 C B:GLY699 4.7 10.7 1.0 N B:LEU700 4.7 10.3 1.0 C B:ASP648 4.7 11.1 1.0 C B:PRO698 4.7 10.7 1.0 CA B:ASP648 4.7 9.4 1.0 CB B:THR650 4.7 12.8 1.0 CE1 B:HIS701 4.8 12.9 1.0 CB B:GLU697 4.8 11.2 1.0 O B:HOH936 4.8 13.0 1.0 CD2 B:HIS701 4.8 12.5 1.0 N B:GLY699 4.8 11.2 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