Sodium 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
Magnesium	(Mg)	5 atoms

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

Sodium binding site 1 out of 3 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na903 b:10.2 occ:1.00 OD1 A:ASP562 2.5 6.3 1.0 OG1 A:THR634 2.7 6.3 1.0 O A:HOH1856 2.8 6.4 1.0 OD1 A:ASN539 2.9 8.0 1.0 O A:HOH1500 3.1 5.9 1.0 O A:HOH1581 3.4 10.0 1.0 CG A:ASP562 3.4 4.7 1.0 CG2 A:THR634 3.5 3.3 1.0 CB A:THR634 3.5 6.9 1.0 CB A:ALA537 3.7 1.9 1.0 CG A:ASN539 3.7 6.1 1.0 CB A:ASP562 3.8 3.0 1.0 CA A:ASP562 3.9 8.7 1.0 ND2 A:ASN539 4.0 4.2 1.0 CB A:ALA572 4.0 3.0 1.0 O A:HOH1566 4.3 15.1 1.0 OD2 A:ASP562 4.5 6.2 1.0 N A:ALA572 4.6 3.2 1.0 O A:HOH1527 4.6 5.7 1.0 O A:HOH1048 4.7 4.3 1.0 O A:HOH1018 4.7 6.2 1.0 N A:ASP562 4.7 3.9 1.0 CB A:ASN539 4.9 3.2 1.0 O A:TYR561 4.9 8.8 1.0 O A:HOH1503 4.9 8.1 1.0 C A:ASP562 4.9 5.3 1.0 CA A:THR634 4.9 3.0 1.0 CA A:ALA572 5.0 3.9 1.0

Sodium binding site 2 out of 3 in the Beta-Galactosidase - Construct 33-930


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na902 b:18.1 occ:1.00 O C:HOH1296 2.4 11.8 1.0 O C:ASN643 2.4 9.9 1.0 OD2 C:ASP675 2.5 17.7 1.0 O C:HOH1517 2.6 18.5 1.0 O C:VAL646 2.6 13.9 1.0 O C:HOH1587 2.6 18.2 1.0 CG C:ASP675 3.3 15.0 1.0 C C:ASN643 3.6 15.1 1.0 CB C:ASP675 3.7 10.2 1.0 C C:VAL646 3.8 11.6 1.0 CA C:ASP644 4.1 20.9 1.0 CA C:HIS647 4.2 16.0 1.0 OD1 C:ASP675 4.3 14.1 1.0 N C:ASP644 4.3 18.0 1.0 ND1 C:HIS647 4.3 18.8 1.0 O C:HOH1524 4.3 28.7 1.0 C C:ASP644 4.4 19.9 1.0 O C:GLN639 4.4 11.4 1.0 N C:HIS647 4.5 8.7 1.0 N C:VAL646 4.6 17.1 1.0 O C:SER640 4.8 6.9 1.0 CA C:ASN643 4.8 14.1 1.0 O C:ASP644 4.8 19.9 1.0 N C:ASP645 4.8 18.8 1.0 CA C:VAL646 4.9 10.1 1.0 C C:HIS647 5.0 11.1 1.0

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


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na903 b:15.9 occ:1.00 O C:ASP595 2.5 8.0 1.0 O C:HOH1393 2.6 15.6 1.0 OD1 C:ASP329 2.8 13.7 1.0 O C:HOH1475 2.9 9.3 1.0 O C:ASP329 3.5 10.9 1.0 C C:ASP595 3.7 10.0 1.0 N C:GLY331 3.8 16.1 1.0 CG C:ASP329 3.9 16.3 1.0 CA C:TYR596 3.9 7.3 1.0 NE2 C:GLN345 4.0 8.8 1.0 C C:ASP329 4.2 14.6 1.0 CB C:PHE594 4.2 9.4 1.0 N C:TYR596 4.3 6.6 1.0 CA C:GLY331 4.3 14.9 1.0 CG2 C:THR627 4.3 12.9 1.0 OD2 C:ASP329 4.4 17.8 1.0 CB C:TYR596 4.4 5.4 1.0 CA C:THR627 4.5 9.4 1.0 O C:HOH1293 4.5 10.5 1.0 CD2 C:PHE594 4.6 10.5 1.0 C C:GLN330 4.6 12.1 1.0 CA C:GLN330 4.7 12.8 1.0 N C:GLN330 4.7 14.7 1.0 CB C:THR627 4.7 16.9 1.0 O C:THR627 4.8 10.8 1.0 C C:PHE594 4.8 8.9 1.0 CA C:ASP595 4.9 10.8 1.0 N C:ASP595 4.9 8.4 1.0 CG C:PHE594 4.9 14.5 1.0 O C:PHE594 5.0 8.9 1.0 C C:TYR596 5.0 10.8 1.0 CB C:ASP329 5.0 11.7 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.