Magnesium in PDB 6tsh: Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin

All present enzymatic activity of Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin:
3.2.1.23;

The binding sites of Magnesium atom in the Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin (pdb code 6tsh). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin, PDB code: 6tsh:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg3001 b:2.2 occ:1.00 OE2 A:GLU416 2.2 10.0 1.0 OE1 A:GLU461 2.2 22.4 1.0 O A:HOH3104 2.2 2.9 1.0 O A:HOH3122 2.3 1.3 1.0 O A:HOH3186 2.3 0.5 1.0 ND1 A:HIS418 2.4 8.3 1.0 CE1 A:HIS418 3.3 9.3 1.0 CD A:GLU416 3.3 8.2 1.0 CD A:GLU461 3.3 28.2 1.0 CG A:HIS418 3.4 6.6 1.0 OE1 A:GLU416 3.7 9.3 1.0 CB A:HIS418 3.7 5.9 1.0 OE2 A:GLU461 3.9 30.3 1.0 OD1 A:ASN102 4.1 10.3 1.0 O4 A:DGJ3002 4.3 5.4 1.0 O A:ASP199 4.3 5.1 1.0 CB A:ASP201 4.3 9.9 1.0 N A:ASP201 4.3 7.3 1.0 CG A:GLU461 4.4 16.3 1.0 C2 A:DGJ3002 4.4 9.1 1.0 NE2 A:HIS418 4.4 8.4 1.0 CB A:GLU461 4.5 10.2 1.0 ND2 A:ASN460 4.5 4.6 1.0 O3 A:DGJ3002 4.5 5.6 1.0 CD2 A:HIS418 4.5 7.8 1.0 CG A:GLU416 4.5 5.5 1.0 O A:ASN102 4.6 9.8 1.0 O2 A:DGJ3002 4.9 10.2 1.0 CA A:ASP201 4.9 7.3 1.0 C A:GLN200 5.0 5.9 1.0 CA A:GLN200 5.0 5.3 1.0 CG2 A:VAL103 5.0 13.0 1.0

Magnesium binding site 2 out of 4 in the Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg3001 b:2.2 occ:1.00 OE2 B:GLU416 2.2 10.0 1.0 OE1 B:GLU461 2.2 22.4 1.0 O B:HOH3104 2.2 2.9 1.0 O B:HOH3123 2.3 1.3 1.0 O B:HOH3186 2.3 0.5 1.0 ND1 B:HIS418 2.4 8.3 1.0 CE1 B:HIS418 3.3 9.3 1.0 CD B:GLU416 3.3 8.2 1.0 CD B:GLU461 3.3 28.2 1.0 CG B:HIS418 3.4 6.6 1.0 OE1 B:GLU416 3.7 9.3 1.0 CB B:HIS418 3.7 5.9 1.0 OE2 B:GLU461 3.9 30.3 1.0 OD1 B:ASN102 4.1 10.3 1.0 O4 B:DGJ3002 4.3 5.4 1.0 O B:ASP199 4.3 5.1 1.0 CB B:ASP201 4.3 9.9 1.0 N B:ASP201 4.3 7.3 1.0 CG B:GLU461 4.4 16.3 1.0 C2 B:DGJ3002 4.4 9.1 1.0 NE2 B:HIS418 4.4 8.4 1.0 CB B:GLU461 4.5 10.2 1.0 ND2 B:ASN460 4.5 4.6 1.0 O3 B:DGJ3002 4.5 5.6 1.0 CD2 B:HIS418 4.5 7.8 1.0 CG B:GLU416 4.5 5.5 1.0 O B:ASN102 4.6 9.8 1.0 O2 B:DGJ3002 4.9 10.2 1.0 CA B:ASP201 4.9 7.3 1.0 C B:GLN200 5.0 5.9 1.0 CA B:GLN200 5.0 5.3 1.0 CG2 B:VAL103 5.0 13.0 1.0

Magnesium binding site 3 out of 4 in the Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg3001 b:2.2 occ:1.00 OE2 C:GLU416 2.2 10.0 1.0 OE1 C:GLU461 2.2 22.4 1.0 O C:HOH3104 2.2 2.9 1.0 O C:HOH3122 2.3 1.3 1.0 O C:HOH3186 2.3 0.5 1.0 ND1 C:HIS418 2.4 8.3 1.0 CE1 C:HIS418 3.3 9.3 1.0 CD C:GLU416 3.3 8.2 1.0 CD C:GLU461 3.3 28.2 1.0 CG C:HIS418 3.4 6.6 1.0 OE1 C:GLU416 3.7 9.3 1.0 CB C:HIS418 3.7 5.9 1.0 OE2 C:GLU461 3.9 30.3 1.0 OD1 C:ASN102 4.1 10.3 1.0 O4 C:DGJ3002 4.3 5.4 1.0 O C:ASP199 4.3 5.1 1.0 CB C:ASP201 4.3 9.9 1.0 N C:ASP201 4.3 7.3 1.0 CG C:GLU461 4.4 16.3 1.0 C2 C:DGJ3002 4.4 9.1 1.0 NE2 C:HIS418 4.4 8.4 1.0 CB C:GLU461 4.5 10.2 1.0 ND2 C:ASN460 4.5 4.6 1.0 O3 C:DGJ3002 4.5 5.6 1.0 CD2 C:HIS418 4.5 7.8 1.0 CG C:GLU416 4.5 5.5 1.0 O C:ASN102 4.6 9.8 1.0 O2 C:DGJ3002 4.9 10.2 1.0 CA C:ASP201 4.9 7.3 1.0 C C:GLN200 5.0 5.9 1.0 CA C:GLN200 5.0 5.3 1.0 CG2 C:VAL103 5.0 13.0 1.0

Magnesium binding site 4 out of 4 in the Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beta-Galactosidase in Complex with Deoxygalacto-Nojirimycin within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg3001 b:2.2 occ:1.00 OE2 D:GLU416 2.2 10.0 1.0 OE1 D:GLU461 2.2 22.4 1.0 O D:HOH3104 2.2 2.9 1.0 O D:HOH3122 2.3 1.3 1.0 O D:HOH3186 2.3 0.5 1.0 ND1 D:HIS418 2.4 8.3 1.0 CE1 D:HIS418 3.3 9.3 1.0 CD D:GLU416 3.3 8.2 1.0 CD D:GLU461 3.3 28.2 1.0 CG D:HIS418 3.4 6.6 1.0 OE1 D:GLU416 3.7 9.3 1.0 CB D:HIS418 3.7 5.9 1.0 OE2 D:GLU461 3.9 30.3 1.0 OD1 D:ASN102 4.1 10.3 1.0 O4 D:DGJ3002 4.3 5.4 1.0 O D:ASP199 4.3 5.1 1.0 CB D:ASP201 4.3 9.9 1.0 N D:ASP201 4.3 7.3 1.0 CG D:GLU461 4.4 16.3 1.0 C2 D:DGJ3002 4.4 9.1 1.0 NE2 D:HIS418 4.4 8.4 1.0 CB D:GLU461 4.5 10.2 1.0 ND2 D:ASN460 4.5 4.6 1.0 O3 D:DGJ3002 4.5 5.6 1.0 CD2 D:HIS418 4.5 7.8 1.0 CG D:GLU416 4.5 5.5 1.0 O D:ASN102 4.6 9.8 1.0 O2 D:DGJ3002 4.9 10.2 1.0 CA D:ASP201 4.9 7.3 1.0 C D:GLN200 5.0 5.9 1.0 CA D:GLN200 5.0 5.3 1.0 CG2 D:VAL103 5.0 13.0 1.0

M.Saur, M.J.Hartshorn, J.Dong, J.Reeks, G.Bunkoczi, H.Jhoti, P.A.Williams. Fragment-Based Drug Discovery Using Cryo-Ems. Drug Discov Today 2019.
ISSN: ESSN 1878-5832
PubMed: 31877353
DOI: 10.1016/J.DRUDIS.2019.12.006