Sodium in PDB 6zju: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose

All present enzymatic activity of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose:
3.2.1.23;

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose, PDB code: 6zju 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)	43.65 / 1.75
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.241, 138.241, 127.568, 90.00, 90.00, 120.00
R / Rfree (%)	17 / 18.2

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose (pdb code 6zju). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose, PDB code: 6zju:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose


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 E441Q in Complex with Saccharose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1109 b:38.4 occ:1.00 O A:PHE581 2.4 36.1 1.0 OD2 A:ASP584 2.4 28.2 1.0 OD2 A:ASP207 2.4 31.8 1.0 O A:HOH1594 2.5 50.3 1.0 O A:HOH1702 2.6 38.0 1.0 CG A:ASP207 3.3 34.5 1.0 CD2 A:PHE581 3.3 52.1 1.0 CG A:ASP584 3.3 29.3 1.0 C A:PHE581 3.4 36.0 1.0 OD1 A:ASP207 3.5 33.0 1.0 OH A:TYR108 3.6 29.2 1.0 CE2 A:PHE581 3.8 54.3 1.0 OD1 A:ASP584 3.9 28.9 1.0 NE1 A:TRP548 4.0 25.9 1.0 CA A:VAL582 4.1 34.6 1.0 O A:HOH1267 4.1 37.3 1.0 N A:VAL582 4.2 35.3 1.0 CG A:PHE581 4.2 46.0 1.0 CB A:ASP584 4.3 29.6 1.0 OE2 A:GLU549 4.4 23.4 1.0 CB A:PHE581 4.5 41.4 1.0 CA A:PHE581 4.5 32.6 1.0 CB A:ASP207 4.6 30.6 1.0 CZ A:TYR108 4.7 31.5 1.0 NE2 A:HIS520 4.8 26.4 1.0 O A:ASP207 4.8 29.4 1.0 C A:VAL582 4.8 34.6 1.0 CE2 A:TRP548 4.8 25.3 1.0 CZ A:PHE581 4.9 53.7 1.0 CD1 A:TRP548 4.9 26.2 1.0 CZ2 A:TRP548 5.0 24.6 1.0

Sodium binding site 2 out of 3 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose


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 E441Q in Complex with Saccharose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:35.2 occ:1.00 O A:HOH1798 2.4 46.9 1.0 O A:HOH1692 2.4 40.6 1.0 O A:LEU542 2.5 27.3 1.0 O A:PHE536 2.5 29.9 1.0 O A:TYR539 2.7 29.2 1.0 C A:TYR539 3.6 29.6 1.0 C A:LEU542 3.6 27.4 1.0 C A:PHE536 3.7 30.8 1.0 CA A:PRO540 3.8 30.4 1.0 O A:PRO540 3.9 26.9 1.0 C A:PRO540 4.0 28.1 1.0 N A:PRO540 4.1 30.3 1.0 CD A:ARG325 4.2 42.3 1.0 N A:LEU542 4.2 25.8 1.0 NE A:ARG325 4.2 46.4 1.0 CB A:LEU542 4.2 28.2 1.0 CA A:LEU542 4.2 26.4 1.0 CA A:PHE536 4.3 28.1 1.0 N A:TYR539 4.6 29.4 1.0 CA A:TYR539 4.7 28.3 1.0 N A:MET543 4.8 28.1 1.0 N A:GLU537 4.8 30.9 1.0 CD1 A:LEU327 4.8 29.6 1.0 N A:ARG541 4.9 26.7 1.0 CG A:ARG325 5.0 36.7 1.0 CA A:GLU537 5.0 34.7 1.0 C A:GLU537 5.0 35.1 1.0 CB A:PHE536 5.0 28.1 1.0

Sodium binding site 3 out of 3 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Saccharose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1111 b:38.1 occ:1.00 OD1 A:ASP651 2.4 36.3 1.0 O A:HOH1821 2.4 40.4 1.0 O A:HOH1775 2.4 33.4 1.0 O A:HOH1938 2.5 42.3 1.0 O A:HOH1817 2.5 43.8 1.0 CG A:ASP651 3.5 36.4 1.0 CA A:ASP651 4.0 36.9 1.0 CB A:ASP651 4.1 36.6 1.0 N A:VAL652 4.2 34.5 1.0 O A:HOH1456 4.2 33.2 1.0 O A:VAL652 4.4 34.5 1.0 OD2 A:ASP651 4.5 37.1 1.0 O A:HOH1304 4.5 32.0 1.0 O A:HOH1335 4.5 46.1 1.0 O A:HOH1845 4.5 37.9 1.0 O A:HOH1796 4.5 56.1 1.0 C A:ASP651 4.6 37.1 1.0 O A:HOH1906 4.7 49.4 1.0 O A:HOH1885 4.9 39.8 1.0 C A:VAL652 5.0 34.4 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