Magnesium in PDB 5xxl: Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron

The structure of Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron, PDB code: 5xxl 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)	29.94 / 1.60
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.940, 167.880, 224.090, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 22.7

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

Magnesium binding site 1 out of 2 in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron


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 GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:20.4 occ:1.00 O A:VAL701 2.1 19.8 1.0 O A:HOH935 2.1 21.5 1.0 O A:HOH1111 2.1 17.8 1.0 O A:HOH938 2.2 21.4 1.0 OD1 A:ASP699 2.2 16.4 1.0 O A:HOH995 2.2 21.0 1.0 CG A:ASP699 3.2 16.6 1.0 C A:VAL701 3.3 18.3 1.0 OD2 A:ASP699 3.5 17.6 1.0 N A:VAL701 3.9 18.6 1.0 CA A:VAL701 4.1 18.4 1.0 O A:PRO749 4.1 21.5 1.0 O A:HOH1369 4.2 36.6 1.0 O A:GLU748 4.2 19.8 1.0 N A:GLY702 4.3 18.1 1.0 O A:GLU751 4.3 21.9 1.0 O A:HOH1104 4.4 24.6 1.0 CA A:GLY702 4.4 18.6 1.0 CB A:VAL701 4.5 18.3 1.0 CA A:GLY750 4.5 21.6 1.0 OE1 A:GLU748 4.5 25.5 1.0 CB A:ASP699 4.5 16.8 1.0 CB A:GLU748 4.6 21.9 1.0 CZ A:PHE752 4.6 20.6 1.0 C A:PRO749 4.7 21.3 1.0 N A:LEU700 4.7 17.7 1.0 C A:ASP699 4.7 17.0 1.0 N A:GLU751 4.8 22.9 1.0 C A:GLY750 4.8 22.2 1.0 CA A:ASP699 4.8 16.9 1.0 N A:GLY750 4.9 21.2 1.0 C A:GLU748 4.9 21.4 1.0 CE1 A:PHE752 4.9 20.6 1.0 O A:HOH1209 5.0 24.1 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron


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 GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:15.9 occ:1.00 O B:VAL701 2.1 16.4 1.0 O B:HOH999 2.1 16.4 1.0 O B:HOH1076 2.1 16.6 1.0 OD1 B:ASP699 2.1 14.8 1.0 O B:HOH988 2.1 17.1 1.0 O B:HOH1050 2.2 18.0 1.0 CG B:ASP699 3.1 13.9 1.0 C B:VAL701 3.3 15.7 1.0 OD2 B:ASP699 3.4 13.4 1.0 N B:VAL701 3.9 15.6 1.0 CA B:VAL701 4.1 15.4 1.0 O B:PRO749 4.2 20.7 1.0 N B:GLY702 4.2 14.9 1.0 O B:HOH1361 4.3 32.5 1.0 O B:GLU748 4.3 20.1 1.0 O B:GLU751 4.4 20.1 1.0 CA B:GLY702 4.4 15.6 1.0 CB B:ASP699 4.4 13.9 1.0 CB B:VAL701 4.5 15.5 1.0 O B:HOH1236 4.5 17.8 1.0 CA B:GLY750 4.5 21.1 1.0 OE1 B:GLU748 4.5 21.3 1.0 C B:ASP699 4.6 14.4 1.0 N B:LEU700 4.6 14.9 1.0 CZ B:PHE752 4.7 17.7 1.0 CB B:GLU748 4.7 21.3 1.0 C B:PRO749 4.8 21.1 1.0 C B:GLY750 4.8 21.5 1.0 N B:GLU751 4.8 21.9 1.0 CA B:ASP699 4.8 13.9 1.0 O B:HOH1187 4.8 16.7 1.0 N B:GLY750 4.9 21.3 1.0 C B:GLU748 5.0 21.4 1.0 CE1 B:PHE752 5.0 17.9 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