Magnesium in PDB 5xxo: Crystal Structure of Mutant (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorotriose

The structure of Crystal Structure of Mutant (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorotriose, PDB code: 5xxo was solved by M.Nakajima, R.Ishiguro, N.Tanaka, K.Abe, T.Maeda, A.Miyanaga, Y.Takahash, N.Sugimoto, H.Nakai, H.Taguchi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.78 / 2.02
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	82.062, 167.887, 225.450, 90.00, 90.00, 90.00
R / Rfree (%)	16.9 / 20.6

The binding sites of Magnesium atom in the Crystal Structure of Mutant (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorotriose (pdb code 5xxo). 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 (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorotriose, PDB code: 5xxo:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Mutant (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron 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 (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorotriose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:20.8 occ:1.00 O A:VAL701 2.1 21.7 1.0 O A:HOH990 2.1 21.0 1.0 O A:HOH1103 2.1 22.2 1.0 OD1 A:ASP699 2.1 19.2 1.0 O A:HOH915 2.2 21.1 1.0 O A:HOH954 2.2 22.2 1.0 CG A:ASP699 3.1 19.3 1.0 C A:VAL701 3.3 22.4 1.0 OD2 A:ASP699 3.4 18.6 1.0 N A:VAL701 3.9 22.5 1.0 O A:HOH1203 4.0 30.6 1.0 O A:PRO749 4.1 25.7 1.0 CA A:VAL701 4.1 22.8 1.0 O A:GLU748 4.3 27.2 1.0 N A:GLY702 4.3 22.5 1.0 O A:GLU751 4.3 26.1 1.0 CA A:GLY702 4.4 22.8 1.0 CB A:VAL701 4.5 23.6 1.0 O A:HOH1177 4.5 19.9 1.0 CA A:GLY750 4.5 25.1 1.0 CB A:ASP699 4.5 19.0 1.0 OE1 A:GLU748 4.5 29.0 1.0 CB A:GLU748 4.6 28.0 1.0 N A:LEU700 4.6 20.9 1.0 C A:PRO749 4.7 26.3 1.0 C A:ASP699 4.7 21.0 1.0 CZ A:PHE752 4.7 22.3 1.0 N A:GLU751 4.7 26.3 1.0 C A:GLY750 4.8 26.0 1.0 N A:GLY750 4.8 24.7 1.0 CA A:ASP699 4.8 19.8 1.0 O A:HOH1144 4.8 25.9 1.0 C A:GLU748 4.9 28.2 1.0 CE1 A:PHE752 4.9 22.2 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mutant (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron 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 (D286N) GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorotriose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:17.8 occ:1.00 O B:VAL701 2.1 18.9 1.0 O B:HOH955 2.1 19.6 1.0 OD1 B:ASP699 2.2 16.1 1.0 O B:HOH969 2.2 18.9 1.0 O B:HOH920 2.2 15.8 1.0 O B:HOH1045 2.2 15.2 1.0 CG B:ASP699 3.2 16.5 1.0 C B:VAL701 3.3 18.8 1.0 OD2 B:ASP699 3.5 15.2 1.0 N B:VAL701 3.9 18.8 1.0 CA B:VAL701 4.1 18.5 1.0 O B:PRO749 4.2 19.3 1.0 N B:GLY702 4.2 17.9 1.0 O B:HOH1196 4.3 30.9 1.0 O B:GLU748 4.3 24.2 1.0 O B:GLU751 4.3 22.7 1.0 CA B:GLY702 4.4 17.7 1.0 OE1 B:GLU748 4.4 24.8 1.0 O B:HOH1181 4.4 20.5 1.0 CB B:VAL701 4.5 18.6 1.0 CB B:ASP699 4.5 16.6 1.0 CA B:GLY750 4.5 21.2 1.0 N B:LEU700 4.6 18.4 1.0 CZ B:PHE752 4.6 21.8 1.0 C B:ASP699 4.7 17.3 1.0 C B:PRO749 4.7 21.0 1.0 N B:GLU751 4.7 22.4 1.0 CB B:GLU748 4.7 25.1 1.0 C B:GLY750 4.7 21.8 1.0 CA B:ASP699 4.8 17.0 1.0 CE1 B:PHE752 4.9 21.9 1.0 N B:GLY750 4.9 21.0 1.0 O B:HOH1123 4.9 12.8 1.0 C B:GLU748 4.9 23.8 1.0

R.Ishiguro, N.Tanaka, K.Abe, M.Nakajima, T.Maeda, A.Miyanaga, Y.Takahashi, N.Sugimoto, H.Nakai, H.Taguchi. Function and Structure Relationships of A Beta-1,2-Glucooligosaccharide-Degrading Beta-Glucosidase. Febs Lett. V. 591 3926 2017.
ISSN: ISSN 1873-3468
PubMed: 29131329
DOI: 10.1002/1873-3468.12911