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

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

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactulose, PDB code: 6zjt 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)	43.79 / 1.97
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.974, 138.974, 127.699, 90.00, 90.00, 120.00
R / Rfree (%)	19.5 / 22.6

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactulose (pdb code 6zjt). 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 E441Q in Complex with Lactulose, PDB code: 6zjt:
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 E441Q 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 E441Q in Complex with Lactulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1107 b:67.8 occ:1.00 O A:PRO914 2.5 56.2 1.0 O A:ALA957 2.6 62.2 1.0 O A:LEU954 2.8 54.8 1.0 O A:ASP955 2.8 59.4 1.0 O A:HOH1268 3.1 49.1 1.0 NH1 A:ARG913 3.2 47.8 1.0 C A:ASP955 3.4 60.2 1.0 C A:PRO914 3.6 55.6 1.0 CA A:ASP955 3.6 57.9 1.0 C A:ALA957 3.8 62.2 1.0 C A:LEU954 3.9 56.1 1.0 N A:ALA957 3.9 61.5 1.0 N A:ASP955 4.2 56.8 1.0 CZ A:ARG913 4.3 48.5 1.0 CA A:ALA957 4.3 61.7 1.0 OD1 A:ASP955 4.3 55.2 1.0 CA A:PRO914 4.3 56.8 1.0 CG A:ARG913 4.3 52.6 1.0 N A:ALA956 4.3 62.3 1.0 CB A:PRO914 4.4 57.5 1.0 N A:PRO914 4.4 55.8 1.0 C A:ALA956 4.4 62.9 1.0 N A:GLN915 4.5 53.3 1.0 CD A:PRO914 4.7 57.2 1.0 CB A:ALA957 4.7 62.0 1.0 CA A:GLN915 4.7 50.8 1.0 CD A:ARG913 4.7 51.6 1.0 N A:ALA958 4.9 63.8 1.0 NE A:ARG913 4.9 50.2 1.0 CA A:ALA956 4.9 63.6 1.0 CB A:ASP955 4.9 57.3 1.0 C A:ARG913 5.0 53.7 1.0 O A:ALA956 5.0 64.0 1.0

Sodium binding site 2 out of 2 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q 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 E441Q in Complex with Lactulose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1108 b:42.3 occ:1.00 O A:HOH1304 2.0 45.8 1.0 OE2 A:GLU393 2.1 45.9 1.0 O A:HOH1255 2.2 48.1 1.0 OE1 A:GLN441 2.2 57.4 1.0 ND1 A:HIS395 2.3 50.1 1.0 CE1 A:HIS395 3.2 50.4 1.0 CD A:GLU393 3.3 46.7 1.0 CG A:HIS395 3.3 50.1 1.0 CD A:GLN441 3.4 54.3 1.0 CB A:HIS395 3.6 46.9 1.0 OE1 A:GLU393 3.8 46.7 1.0 C2 B:GAL2 4.0 52.7 0.7 CB A:GLN441 4.2 47.5 1.0 NE2 A:GLN441 4.2 50.3 1.0 O3 B:GAL2 4.2 51.8 0.7 O4 B:GAL2 4.2 53.9 0.7 O A:ASP205 4.3 51.9 1.0 OD1 A:ASN110 4.3 53.9 1.0 CG A:GLN441 4.3 50.6 1.0 NE2 A:HIS395 4.3 50.2 1.0 CB A:ASP207 4.4 48.6 1.0 O4 B:FRU1 4.4 53.8 0.7 CG A:GLU393 4.4 44.9 1.0 N A:ASP207 4.4 48.2 1.0 CD2 A:HIS395 4.4 50.3 1.0 ND2 A:ASN440 4.5 43.3 1.0 O2 B:GAL2 4.5 51.5 0.7 O A:ASN110 4.5 56.8 1.0 C3 B:GAL2 4.6 52.9 0.7 CG2 A:VAL111 4.7 55.6 1.0 C1 B:GAL2 4.8 53.2 0.7 CA A:ASP207 4.9 48.0 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