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

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

Resolution Low / High (Å)	46.74 / 2.05
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.977, 167.909, 225.061, 90.00, 90.00, 90.00
R / Rfree (%)	17.8 / 21.9

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

Magnesium binding site 1 out of 2 in the Crystal Structure of Mutant (D286N) Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorose


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) Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:20.8 occ:1.00 O A:VAL701 2.1 21.6 1.0 O A:HOH1036 2.1 21.3 1.0 O A:HOH957 2.2 18.9 1.0 OD1 A:ASP699 2.2 19.1 1.0 O A:HOH984 2.2 18.6 1.0 O A:HOH1065 2.2 18.3 1.0 CG A:ASP699 3.1 19.5 1.0 C A:VAL701 3.3 21.8 1.0 OD2 A:ASP699 3.5 18.4 1.0 N A:VAL701 3.8 23.2 1.0 O A:PRO749 4.0 20.8 1.0 CA A:VAL701 4.0 22.3 1.0 O A:HOH1120 4.3 18.7 1.0 N A:GLY702 4.3 20.3 1.0 O A:GLU748 4.3 22.3 1.0 O A:GLU751 4.4 18.6 1.0 CA A:GLY702 4.4 19.9 1.0 CA A:GLY750 4.4 20.6 1.0 CB A:VAL701 4.4 22.2 1.0 CB A:ASP699 4.5 19.9 1.0 OE1 A:GLU748 4.6 26.4 1.0 N A:LEU700 4.6 22.1 1.0 C A:PRO749 4.7 20.9 1.0 C A:ASP699 4.7 21.0 1.0 CZ A:PHE752 4.7 20.4 1.0 CB A:GLU748 4.7 24.5 1.0 C A:GLY750 4.8 21.5 1.0 N A:GLU751 4.8 22.6 1.0 CA A:ASP699 4.8 20.3 1.0 N A:GLY750 4.9 20.4 1.0 O A:HOH1167 4.9 19.1 1.0 CE1 A:PHE752 4.9 20.3 1.0 C A:GLU748 4.9 23.5 1.0 C A:LEU700 4.9 23.3 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Mutant (D286N) Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorose


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) Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Sophorose within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:18.4 occ:1.00 O B:VAL701 2.1 19.9 1.0 OD1 B:ASP699 2.1 18.2 1.0 O B:HOH902 2.1 15.3 1.0 O B:HOH928 2.2 20.8 1.0 O B:HOH948 2.2 25.2 1.0 O B:HOH1063 2.2 19.3 1.0 CG B:ASP699 3.1 18.5 1.0 C B:VAL701 3.3 19.0 1.0 OD2 B:ASP699 3.4 17.8 1.0 N B:VAL701 4.0 18.9 1.0 O B:PRO749 4.1 20.8 1.0 O B:HOH1228 4.1 30.2 1.0 CA B:VAL701 4.2 18.5 1.0 N B:GLY702 4.2 18.8 1.0 O B:GLU748 4.3 24.6 1.0 CA B:GLY702 4.3 18.8 1.0 OE1 B:GLU748 4.3 26.5 1.0 CA B:GLY750 4.4 23.2 1.0 CB B:ASP699 4.5 18.4 1.0 O B:GLU751 4.5 23.5 1.0 CB B:VAL701 4.5 18.5 1.0 O B:HOH978 4.6 23.4 1.0 N B:LEU700 4.6 19.9 1.0 CB B:GLU748 4.6 27.1 1.0 C B:PRO749 4.7 22.4 1.0 C B:ASP699 4.7 19.5 1.0 CZ B:PHE752 4.7 22.7 1.0 C B:GLY750 4.7 23.7 1.0 N B:GLU751 4.7 24.3 1.0 O B:HOH1141 4.8 21.3 1.0 CA B:ASP699 4.8 18.6 1.0 N B:GLY750 4.8 22.1 1.0 C B:GLU748 4.9 24.9 1.0 CE1 B:PHE752 5.0 23.2 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