Magnesium in PDB 5dmy: Beta-Galactosidase - Construct 33-930

All present enzymatic activity of Beta-Galactosidase - Construct 33-930:
3.2.1.23;

The structure of Beta-Galactosidase - Construct 33-930, PDB code: 5dmy was solved by K.A.Watson, A.Lazidou, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.93 / 1.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	153.040, 52.650, 153.329, 90.00, 91.64, 90.00
R / Rfree (%)	19.8 / 26.4

The structure of Beta-Galactosidase - Construct 33-930 also contains other interesting chemical elements:

Nickel	(Ni)	1 atom
Sodium	(Na)	3 atoms

The binding sites of Magnesium atom in the Beta-Galactosidase - Construct 33-930 (pdb code 5dmy). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 5 binding sites of Magnesium where determined in the Beta-Galactosidase - Construct 33-930, PDB code: 5dmy:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5;

Magnesium binding site 1 out of 5 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg901 b:8.2 occ:1.00 O A:VAL646 2.2 9.9 1.0 O A:ASN643 2.3 4.2 1.0 O A:HOH1331 2.4 5.6 1.0 O A:HOH1703 2.5 12.9 1.0 O A:HOH1682 2.5 17.8 1.0 OD2 A:ASP675 2.6 6.9 1.0 CG A:ASP675 3.4 6.4 1.0 C A:VAL646 3.4 6.5 1.0 C A:ASN643 3.5 6.5 1.0 CB A:ASP675 3.9 7.4 1.0 CA A:ASP644 4.0 9.9 1.0 CA A:HIS647 4.0 6.6 1.0 O A:HOH1309 4.0 16.9 1.0 N A:HIS647 4.2 6.5 1.0 N A:ASP644 4.2 9.5 1.0 OD1 A:ASP675 4.2 5.3 1.0 ND1 A:HIS647 4.2 8.3 1.0 N A:VAL646 4.3 9.8 1.0 O A:GLN639 4.4 2.9 1.0 C A:ASP644 4.4 10.8 1.0 CA A:VAL646 4.5 8.1 1.0 CA A:ASN643 4.6 5.3 1.0 CG2 A:VAL646 4.7 7.1 1.0 OD1 A:ASP644 4.7 24.5 1.0 N A:ASP645 4.7 8.3 1.0 C A:HIS647 4.8 5.2 1.0 CB A:ASN643 4.9 5.2 1.0 N A:ASN643 4.9 3.6 1.0 N A:THR648 4.9 6.1 1.0 OG1 A:THR648 4.9 4.5 1.0 CE1 A:HIS647 5.0 9.7 1.0 CG A:HIS647 5.0 9.8 1.0 O A:ASP644 5.0 9.7 1.0

Magnesium binding site 2 out of 5 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg902 b:10.2 occ:1.00 OE1 A:GLN330 2.6 3.4 1.0 O A:HOH1396 2.7 3.8 1.0 O A:HOH1184 2.7 3.7 1.0 O A:HOH1269 3.0 3.2 1.0 NE2 A:GLN345 3.4 2.4 1.0 CA A:GLN330 3.5 4.0 1.0 CD A:GLN330 3.5 4.1 1.0 CB A:GLN330 3.6 2.6 1.0 CG A:GLN345 3.7 2.0 1.0 O A:HOH1327 3.7 4.9 1.0 CD A:GLN345 3.7 2.0 1.0 C A:GLN330 3.8 3.3 1.0 O A:GLN330 3.9 3.6 1.0 O A:ALA341 4.0 2.9 1.0 CG A:GLN330 4.2 8.5 1.0 CB A:ALA341 4.4 1.8 1.0 OH A:TYR789 4.4 3.1 1.0 C A:ALA341 4.5 2.5 1.0 NE2 A:GLN330 4.5 6.8 1.0 N A:GLY331 4.5 3.1 1.0 OE1 A:GLN345 4.6 1.4 1.0 O A:THR627 4.7 3.8 1.0 NH1 A:ARG344 4.7 2.7 1.0 CA A:ALA341 4.7 2.4 1.0 CE2 A:PHE594 4.8 4.8 1.0 N A:GLN330 4.9 4.6 1.0 O A:ASP329 4.9 4.3 1.0 CD2 A:PHE594 5.0 4.4 1.0

Magnesium binding site 3 out of 5 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg901 b:9.5 occ:1.00 OD1 B:ASN394 2.1 15.9 1.0 O B:THR606 2.3 16.7 1.0 O B:HOH1167 2.4 18.7 1.0 O B:ASN392 2.5 15.1 1.0 OE1 B:GLU79 2.6 16.5 1.0 OE1 B:GLU81 2.7 17.7 1.0 CG B:ASN394 3.2 13.2 1.0 C B:THR606 3.4 18.5 1.0 CD B:GLU79 3.4 17.0 1.0 OE2 B:GLU79 3.6 16.2 1.0 C B:ASN392 3.6 16.7 1.0 ND2 B:ASN394 3.8 8.4 1.0 CD B:GLU81 3.9 14.4 1.0 C B:GLY393 4.1 15.9 1.0 CA B:THR606 4.1 19.4 1.0 O B:HOH1508 4.1 18.2 1.0 O B:HOH1165 4.2 15.0 1.0 N B:ASN394 4.2 10.2 1.0 CB B:ASN392 4.2 12.0 1.0 O B:GLY393 4.3 20.9 1.0 CB B:PRO162 4.4 12.0 1.0 CB B:THR606 4.4 18.2 1.0 CB B:ASN394 4.4 13.2 1.0 N B:GLY393 4.5 13.3 1.0 CA B:GLY393 4.5 11.5 1.0 N B:GLY607 4.5 19.5 1.0 CA B:ASN394 4.5 13.8 1.0 CA B:ASN392 4.6 18.0 1.0 OE2 B:GLU81 4.7 12.6 1.0 CA B:GLY607 4.7 19.2 1.0 CG B:GLU81 4.8 21.2 1.0 CG B:GLU79 4.8 15.1 1.0

Magnesium binding site 4 out of 5 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg902 b:12.8 occ:1.00 O B:VAL646 2.3 15.5 1.0 O B:HOH1346 2.3 7.1 1.0 O B:HOH1457 2.4 9.9 1.0 O B:ASN643 2.4 12.7 1.0 OD2 B:ASP675 2.5 9.3 1.0 O B:HOH1244 3.1 25.1 1.0 CG B:ASP675 3.2 12.3 1.0 C B:VAL646 3.4 11.0 1.0 C B:ASN643 3.6 13.3 1.0 CB B:ASP675 3.8 12.8 1.0 CA B:HIS647 4.0 11.3 1.0 OD1 B:ASP675 4.0 12.7 1.0 CA B:ASP644 4.1 13.2 1.0 N B:HIS647 4.2 13.6 1.0 ND1 B:HIS647 4.3 15.1 1.0 N B:ASP644 4.3 11.8 1.0 N B:VAL646 4.4 15.6 1.0 OD1 B:ASP644 4.5 32.2 1.0 O B:GLN639 4.5 9.1 1.0 C B:ASP644 4.5 16.2 1.0 CA B:VAL646 4.5 14.4 1.0 C B:HIS647 4.7 12.2 1.0 CG2 B:VAL646 4.7 11.9 1.0 N B:THR648 4.8 9.2 1.0 CA B:ASN643 4.8 12.2 1.0 N B:ASP645 4.8 13.1 1.0 O B:SER640 5.0 11.8 1.0 CG B:HIS647 5.0 17.0 1.0 CB B:HIS647 5.0 17.9 1.0

Magnesium binding site 5 out of 5 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg901 b:9.5 occ:1.00 O C:HOH1001 1.7 16.8 1.0 O C:THR606 2.2 11.0 1.0 O C:ASN392 2.3 16.4 1.0 OD1 C:ASN394 2.4 10.8 1.0 OE1 C:GLU81 2.4 7.2 1.0 O C:HOH1254 2.5 10.9 1.0 OE1 C:GLU79 2.7 18.0 1.0 C C:THR606 3.3 18.5 1.0 CD C:GLU81 3.5 17.4 1.0 CG C:ASN394 3.5 10.6 1.0 C C:ASN392 3.6 14.9 1.0 CD C:GLU79 3.6 22.0 1.0 OE2 C:GLU79 3.7 16.3 1.0 O C:HOH1408 3.8 20.0 1.0 CA C:THR606 3.9 16.6 1.0 CB C:ASN392 4.0 13.1 1.0 ND2 C:ASN394 4.1 12.1 1.0 CB C:THR606 4.2 25.6 1.0 O C:HOH1161 4.2 22.2 1.0 C C:GLY393 4.2 12.0 1.0 OE2 C:GLU81 4.2 18.6 1.0 N C:ASN394 4.3 11.2 1.0 N C:GLY607 4.4 15.5 1.0 CA C:ASN392 4.4 11.5 1.0 O C:GLY393 4.4 13.6 1.0 CG C:GLU81 4.5 24.0 1.0 CB C:PRO162 4.5 13.9 1.0 N C:GLY393 4.5 11.3 1.0 CA C:GLY393 4.5 10.7 1.0 CA C:ASN394 4.7 11.7 1.0 CB C:ASN394 4.7 11.4 1.0 CA C:GLY607 4.7 16.9 1.0 CB C:GLU81 4.9 16.6 1.0 CG C:PRO162 4.9 15.3 1.0 CG C:GLU79 4.9 13.0 1.0

A.Lazidou, D.Charalampopoulos, K.A.Watson. Rational Protein Engineering Toward the Development of A Beta-Galactosidase with Improved Functional Properties To Be Published.