Magnesium in PDB 9j6m: Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form

The structure of Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form, PDB code: 9j6m was solved by N.Fujio, C.Yamada, K.Takegawa, S.Fushinobu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.50 / 1.80
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	84.551, 57.346, 110.476, 90, 92.05, 90
R / Rfree (%)	14.3 / 17.7

The binding sites of Magnesium atom in the Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form (pdb code 9j6m). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form, PDB code: 9j6m:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:10.1 occ:1.00 OD2 A:ASP157 2.1 9.0 1.0 OD2 A:ASP201 2.1 9.7 1.0 O A:HOH867 2.1 10.0 1.0 O A:ALA231 2.1 9.0 1.0 OE1 A:GLN213 2.1 8.7 1.0 O A:HOH939 2.1 7.2 1.0 CG A:ASP157 3.0 10.1 1.0 CG A:ASP201 3.0 9.7 1.0 CD A:GLN213 3.1 9.0 1.0 C A:ALA231 3.1 8.9 1.0 NE2 A:GLN213 3.4 9.0 1.0 OD1 A:ASP201 3.4 9.5 1.0 CB A:ASP157 3.7 9.4 1.0 N A:ALA231 3.8 9.8 1.0 OD1 A:ASP157 3.9 11.3 1.0 CA A:ALA231 3.9 9.2 1.0 N A:SER232 4.0 9.8 1.0 O A:HOH922 4.1 11.9 1.0 CA A:SER232 4.2 10.4 1.0 OG A:SER232 4.3 11.8 1.0 OG1 A:THR203 4.3 11.4 1.0 CB A:ASP201 4.3 9.7 1.0 CB A:ALA231 4.3 8.9 1.0 CG A:GLN213 4.4 9.1 1.0 CB A:GLN213 4.7 9.7 1.0 CB A:SER232 4.8 10.4 1.0 CG2 A:THR203 4.8 11.8 1.0 O A:ASP157 4.8 8.3 1.0 C A:ASP157 4.9 8.6 1.0 CA A:ASP157 4.9 8.7 1.0 C A:ALA230 5.0 10.6 1.0 CB A:THR203 5.0 11.6 1.0

Magnesium binding site 2 out of 2 in the Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-D-Galactofuranosidase ORF1110 From Streptomyces Sp. JHA19, Ligand-Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg702 b:10.9 occ:1.00 OD2 B:ASP157 2.1 12.6 1.0 O B:HOH877 2.1 9.9 1.0 OE1 B:GLN213 2.1 12.7 1.0 O B:ALA231 2.1 11.5 1.0 OD2 B:ASP201 2.1 11.7 1.0 O B:HOH855 2.2 10.0 1.0 CG B:ASP157 3.0 12.6 1.0 CG B:ASP201 3.0 11.8 1.0 CD B:GLN213 3.1 12.5 1.0 C B:ALA231 3.1 11.5 1.0 OD1 B:ASP201 3.3 13.6 1.0 NE2 B:GLN213 3.4 12.9 1.0 CB B:ASP157 3.7 11.6 1.0 OD1 B:ASP157 3.8 13.0 1.0 N B:ALA231 3.9 13.1 1.0 CA B:ALA231 4.0 12.3 1.0 N B:SER232 4.0 12.4 1.0 O B:HOH948 4.1 10.6 1.0 CA B:SER232 4.2 12.8 1.0 OG B:SER232 4.3 12.2 1.0 OG1 B:THR203 4.3 12.3 1.0 CB B:ASP201 4.3 11.5 1.0 CB B:ALA231 4.4 12.6 1.0 CG B:GLN213 4.4 11.8 1.0 O B:ASP157 4.7 12.4 1.0 CB B:SER232 4.7 11.8 1.0 CB B:GLN213 4.8 12.2 1.0 C B:ASP157 4.8 11.9 1.0 CA B:ASP157 4.9 12.1 1.0 CG2 B:THR203 4.9 12.8 1.0 CB B:THR203 5.0 13.2 1.0

N.Fujio, C.Yamada, T.Kashima, E.Matsunaga, R.J.Nash, K.Takegawa, S.Fushinobu. Crystal Structure of Beta-D-Galactofuranosidase From Streptomyces Sp. JHA19 in Complex with An Inhibitor Provides Insights Into Substrate Specificity. Febs Lett. 2024.
ISSN: ISSN 0014-5793
PubMed: 39543437
DOI: 10.1002/1873-3468.15056