Sodium in PDB 6zjr: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose

All present enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose:
3.2.1.23;

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose, PDB code: 6zjr was solved by M.Rutkiewicz, A.Bujacz, G.Bujacz, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.69 / 2.00
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.427, 137.427, 127.253, 90.00, 90.00, 120.00
R / Rfree (%)	18.3 / 21

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose (pdb code 6zjr). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose, PDB code: 6zjr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:38.9 occ:1.00 OD2 A:ASP584 2.3 35.6 1.0 OD2 A:ASP207 2.4 39.9 1.0 O A:PHE581 2.5 42.6 1.0 O6 B:GAL2 2.6 38.2 1.0 O A:HOH1588 2.6 40.8 1.0 CG A:ASP207 3.4 39.8 1.0 CG A:ASP584 3.4 36.7 1.0 CD2 A:PHE581 3.5 45.0 1.0 C A:PHE581 3.6 43.2 1.0 OD1 A:ASP207 3.8 41.4 1.0 C6 B:GAL2 3.8 39.1 1.0 NE1 A:TRP548 3.9 36.9 1.0 OH A:TYR108 4.0 41.6 1.0 CE2 A:PHE581 4.0 47.2 1.0 O4 B:GAL2 4.0 37.1 1.0 OD1 A:ASP584 4.1 36.2 1.0 CA A:VAL582 4.2 42.3 1.0 C4 B:GAL2 4.3 38.5 1.0 CB A:ASP584 4.3 37.7 1.0 CG A:PHE581 4.3 42.2 1.0 N A:VAL582 4.4 41.9 1.0 NE2 A:HIS520 4.5 35.5 1.0 C5 B:GAL2 4.5 39.0 1.0 OE2 A:GLU549 4.5 35.9 1.0 CB A:ASP207 4.6 36.7 1.0 CB A:PHE581 4.6 41.0 1.0 CA A:PHE581 4.6 42.0 1.0 CD1 A:TRP548 4.8 35.7 1.0 CE2 A:TRP548 4.8 34.7 1.0 CZ2 A:TRP548 5.0 34.8 1.0 C A:VAL582 5.0 41.3 1.0

Sodium binding site 2 out of 2 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q in Complex with Lactulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:68.7 occ:1.00 O A:HOH1708 2.3 53.7 1.0 OD1 A:ASP651 2.3 57.4 1.0 O A:HOH1589 2.4 51.1 1.0 O A:HOH1636 2.6 62.2 1.0 CG A:ASP651 3.3 59.1 1.0 CA A:ASP651 3.7 55.0 1.0 CB A:ASP651 3.7 58.6 1.0 N A:VAL652 3.8 51.8 1.0 C A:ASP651 4.2 53.9 1.0 O A:HOH1567 4.2 49.3 1.0 O A:HOH1502 4.3 51.2 1.0 O A:VAL652 4.4 50.4 1.0 OD2 A:ASP651 4.5 57.6 1.0 C A:VAL652 4.7 51.0 1.0 CA A:VAL652 4.9 51.1 1.0 N A:ASP651 4.9 54.5 1.0 O A:VAL650 5.0 52.3 1.0

M.Rutkiewicz, M.Wanarska, A.Bujacz. Mapping the Transglycosylation Relevant Sites of Cold-Adapted Beta-D-Galactosidase Fromarthrobactersp. 32CB. Int J Mol Sci V. 21 2020.
ISSN: ESSN 1422-0067
PubMed: 32731412
DOI: 10.3390/IJMS21155354