Nickel 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:

Magnesium	(Mg)	5 atoms
Sodium	(Na)	3 atoms

The binding sites of Nickel atom in the Beta-Galactosidase - Construct 33-930 (pdb code 5dmy). This binding sites where shown within 5.0 Angstroms radius around Nickel atom.
In total only one binding site of Nickel was determined in the Beta-Galactosidase - Construct 33-930, PDB code: 5dmy:

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


Mono view


Stereo pair view

A full contact list of Nickel with other atoms in the Ni binding site number 1 of Beta-Galactosidase - Construct 33-930 within 5.0Å range: probe atom residue distance (Å) B Occ A:Ni904 b:24.2 occ:1.00 O A:THR606 2.4 14.3 1.0 O A:HOH1202 2.4 7.5 1.0 OD1 A:ASN394 2.5 4.2 1.0 OE1 A:GLU79 2.6 13.4 1.0 OE1 A:GLU81 2.7 10.4 1.0 O A:ASN392 2.8 11.5 1.0 CD A:GLU79 3.3 15.2 1.0 C A:THR606 3.4 19.8 1.0 OE2 A:GLU79 3.5 8.3 1.0 CG A:ASN394 3.5 4.0 1.0 CD A:GLU81 3.9 11.9 1.0 C A:ASN392 3.9 6.5 1.0 CA A:THR606 4.0 19.7 1.0 ND2 A:ASN394 4.0 9.3 1.0 O A:HOH1083 4.1 15.5 1.0 O A:HOH1605 4.2 19.2 1.0 CB A:THR606 4.3 19.6 1.0 C A:GLY393 4.3 11.1 1.0 CB A:ASN392 4.3 11.6 1.0 CB A:PRO162 4.4 6.9 1.0 N A:ASN394 4.4 8.4 1.0 O A:GLY393 4.5 8.2 1.0 N A:GLY607 4.5 15.5 1.0 OE2 A:GLU81 4.6 15.0 1.0 CA A:GLY393 4.7 8.5 1.0 CA A:ASN394 4.7 5.6 1.0 CG A:GLU79 4.7 10.1 1.0 CB A:ASN394 4.7 4.1 1.0 N A:GLY393 4.7 8.4 1.0 CA A:GLY607 4.7 12.0 1.0 CA A:ASN392 4.8 7.3 1.0 CG A:PRO162 4.8 5.3 1.0 CG A:GLU81 4.8 13.5 1.0 CB A:GLU81 4.8 6.5 1.0 O A:HOH1077 4.9 13.6 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.