Sodium in PDB 6zjp: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q

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

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q, PDB code: 6zjp 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)	43.55 / 1.85
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.996, 137.996, 127.219, 90.00, 90.00, 120.00
R / Rfree (%)	16.2 / 18.9

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q (pdb code 6zjp). 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 E517Q, PDB code: 6zjp:
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 E517Q


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:44.4 occ:1.00 OD2 A:ASP207 2.4 39.0 1.0 OD2 A:ASP584 2.4 32.3 1.0 O A:PHE581 2.5 39.6 1.0 O A:HOH1598 2.6 44.4 1.0 O A:HOH1681 3.0 65.3 1.0 CG A:ASP207 3.3 52.8 1.0 CG A:ASP584 3.4 37.8 1.0 C A:PHE581 3.5 42.4 1.0 OD1 A:ASP207 3.5 40.1 1.0 OH A:TYR108 3.7 36.9 1.0 NE1 A:TRP548 3.8 32.3 1.0 OD1 A:ASP584 4.0 33.4 1.0 O A:HOH1588 4.1 47.0 1.0 CA A:VAL582 4.1 41.2 1.0 N A:VAL582 4.2 37.6 1.0 OE2 A:GLU549 4.2 28.8 1.0 CB A:ASP584 4.5 34.7 1.0 CB A:PHE581 4.5 46.4 1.0 CA A:PHE581 4.5 41.0 1.0 CB A:ASP207 4.6 61.7 1.0 CE2 A:TRP548 4.6 28.3 1.0 CZ2 A:TRP548 4.7 29.7 1.0 NE2 A:HIS520 4.8 33.2 1.0 O A:ASP207 4.8 33.4 1.0 C A:VAL582 4.8 36.6 1.0 CD1 A:TRP548 4.8 30.5 1.0 CZ A:TYR108 4.8 43.2 1.0 CD2 A:PHE581 4.9 48.4 1.0

Sodium binding site 2 out of 3 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:43.0 occ:1.00 O A:ALA957 2.5 38.5 1.0 O A:PRO914 2.5 33.5 1.0 O A:LEU954 2.6 34.0 1.0 O A:ASP955 2.8 40.2 1.0 O A:HOH1753 2.9 39.5 1.0 O A:HOH1538 3.2 36.1 1.0 C A:ASP955 3.3 38.7 1.0 NH2 A:ARG913 3.4 33.7 1.0 C A:ALA957 3.6 40.2 1.0 C A:PRO914 3.6 34.6 1.0 CA A:ASP955 3.6 37.1 1.0 C A:LEU954 3.7 35.2 1.0 N A:ALA957 3.8 35.9 1.0 CA A:ALA957 4.1 38.6 1.0 N A:ASP955 4.2 36.3 1.0 N A:ALA956 4.3 34.6 1.0 C A:ALA956 4.3 41.1 1.0 CB A:PRO914 4.4 36.1 1.0 CA A:PRO914 4.4 33.0 1.0 N A:PRO914 4.4 32.3 1.0 CG A:ARG913 4.5 31.3 1.0 CZ A:ARG913 4.5 33.8 1.0 CB A:ALA957 4.5 35.3 1.0 N A:GLN915 4.5 31.9 1.0 OD1 A:ASP955 4.5 35.1 1.0 O A:HOH1582 4.6 51.9 1.0 CD A:PRO914 4.6 33.5 1.0 N A:ALA958 4.7 37.1 1.0 CA A:GLN915 4.7 29.5 1.0 CA A:ALA956 4.8 42.1 1.0 O A:ALA956 4.9 41.1 1.0 CD A:ARG913 5.0 29.9 1.0 CG A:PRO914 5.0 33.6 1.0 CB A:ASP955 5.0 33.4 1.0 C A:ARG913 5.0 35.1 1.0

Sodium binding site 3 out of 3 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E517Q


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 E517Q within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:22.6 occ:1.00 OE2 A:GLU441 2.2 36.7 1.0 OE2 A:GLU393 2.2 34.9 1.0 O A:HOH1275 2.3 33.0 1.0 O A:HOH1269 2.4 39.6 1.0 ND1 A:HIS395 2.4 46.6 1.0 O A:HOH1570 2.4 33.1 1.0 CD A:GLU441 3.1 36.2 1.0 CE1 A:HIS395 3.2 48.8 1.0 CD A:GLU393 3.4 29.4 1.0 CG A:HIS395 3.5 43.3 1.0 OE1 A:GLU441 3.8 33.8 1.0 CB A:HIS395 3.8 30.0 1.0 OE1 A:GLU393 3.9 32.2 1.0 CG A:GLU441 4.1 33.5 1.0 CB A:GLU441 4.1 27.7 1.0 ND2 A:ASN440 4.1 25.6 1.0 O A:HOH1377 4.2 35.0 1.0 OD1 A:ASN110 4.3 39.2 1.0 CB A:ASP207 4.3 61.7 1.0 NE2 A:HIS395 4.4 44.7 1.0 N A:ASP207 4.5 42.5 1.0 CD2 A:HIS395 4.6 47.3 1.0 O A:ASP205 4.6 38.0 1.0 CG A:GLU393 4.6 23.7 1.0 CG2 A:VAL111 4.6 37.4 1.0 O A:ASN110 4.7 38.7 1.0 O A:HOH1588 5.0 47.0 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