Magnesium in PDB 5xxm: Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Gluconolactone

The structure of Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Gluconolactone, PDB code: 5xxm 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)	42.70 / 1.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	81.820, 167.690, 224.900, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 20.8

The binding sites of Magnesium atom in the Crystal Structure of GH3 Beta-Glucosidase From Bacteroides Thetaiotaomicron in Complex with Gluconolactone (pdb code 5xxm). 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 in Complex with Gluconolactone, PDB code: 5xxm:
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 in Complex with Gluconolactone


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 in Complex with Gluconolactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg801 b:28.1 occ:1.00 O A:HOH942 1.8 26.0 1.0 O A:VAL701 2.1 16.5 1.0 O A:HOH947 2.2 22.1 1.0 OD1 A:ASP699 2.3 14.4 1.0 O A:HOH1083 2.3 16.2 1.0 O A:HOH916 2.3 23.6 1.0 CG A:ASP699 3.3 14.9 1.0 C A:VAL701 3.3 16.4 1.0 OD2 A:ASP699 3.5 15.4 1.0 O A:PRO749 3.9 19.3 1.0 N A:VAL701 4.0 16.1 1.0 O A:GLU748 4.0 19.2 1.0 CA A:VAL701 4.1 16.3 1.0 O A:HOH1270 4.2 30.5 1.0 N A:GLY702 4.3 16.1 1.0 CA A:GLY750 4.4 19.4 1.0 CB A:GLU748 4.4 20.6 1.0 CA A:GLY702 4.4 16.4 1.0 C A:PRO749 4.5 18.8 1.0 O A:HOH1136 4.5 20.7 1.0 CB A:VAL701 4.5 16.2 1.0 CZ A:PHE752 4.5 18.0 1.0 O A:GLU751 4.5 19.1 1.0 OE1 A:GLU748 4.5 23.4 1.0 C A:GLU748 4.6 19.7 1.0 CB A:ASP699 4.6 15.0 1.0 CE1 A:PHE752 4.7 18.3 1.0 N A:GLY750 4.7 18.9 1.0 C A:GLY750 4.8 19.7 1.0 N A:LEU700 4.8 16.0 1.0 C A:ASP699 4.8 15.5 1.0 O A:HOH1238 4.9 18.6 1.0 N A:GLU751 4.9 20.3 1.0 CA A:ASP699 5.0 15.1 1.0

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


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 in Complex with Gluconolactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg801 b:21.4 occ:1.00 O B:HOH1035 1.9 20.1 1.0 O B:VAL701 2.1 15.3 1.0 OD1 B:ASP699 2.1 13.1 1.0 O B:HOH1038 2.1 19.2 1.0 O B:HOH1042 2.2 22.5 1.0 O B:HOH1046 2.3 12.5 1.0 CG B:ASP699 3.1 12.9 1.0 C B:VAL701 3.3 14.5 1.0 OD2 B:ASP699 3.5 12.7 1.0 N B:VAL701 3.9 14.0 1.0 O B:PRO749 4.1 19.7 1.0 CA B:VAL701 4.1 14.3 1.0 O B:GLU748 4.1 19.2 1.0 N B:GLY702 4.3 13.8 1.0 CA B:GLY702 4.4 13.8 1.0 CA B:GLY750 4.4 19.9 1.0 O B:GLU751 4.4 18.7 1.0 O B:HOH1297 4.5 28.3 1.0 CB B:ASP699 4.5 12.7 1.0 CB B:VAL701 4.5 14.5 1.0 CZ B:PHE752 4.5 16.6 1.0 O B:HOH1220 4.6 16.5 1.0 OE1 B:GLU748 4.6 20.9 1.0 CB B:GLU748 4.6 20.8 1.0 N B:LEU700 4.7 13.5 1.0 C B:PRO749 4.7 20.2 1.0 C B:ASP699 4.7 13.1 1.0 O B:HOH1192 4.8 15.1 1.0 C B:GLY750 4.8 19.9 1.0 CA B:ASP699 4.8 12.7 1.0 C B:GLU748 4.8 20.3 1.0 CE1 B:PHE752 4.8 16.7 1.0 N B:GLU751 4.9 20.0 1.0 N B:GLY750 4.9 19.7 1.0 CE2 B:PHE752 5.0 16.6 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