Sodium in PDB 6sed: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Galactose

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

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

Resolution Low / High (Å)	46.52 / 2.23
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	136.875, 136.875, 126.833, 90.00, 90.00, 120.00
R / Rfree (%)	16.5 / 20.4

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


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 in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1115 b:39.9 occ:1.00 OD2 A:ASP584 2.3 31.7 1.0 O A:PHE581 2.4 54.4 1.0 O A:HOH1215 2.4 57.9 1.0 OD2 A:ASP207 2.5 42.5 1.0 O A:HOH1602 2.6 36.0 1.0 CG A:ASP584 3.3 32.0 1.0 CG A:ASP207 3.4 42.1 1.0 C A:PHE581 3.5 51.7 1.0 NE1 A:TRP548 3.7 34.0 1.0 O3 A:GAL1101 3.8 67.9 0.7 OD1 A:ASP207 3.8 65.2 1.0 OD1 A:ASP584 3.8 31.9 1.0 OH A:TYR108 3.9 50.3 1.0 CA A:VAL582 4.1 53.5 1.0 N A:VAL582 4.2 52.4 1.0 CB A:ASP584 4.3 29.3 1.0 CB A:PHE581 4.5 32.1 1.0 CA A:PHE581 4.5 56.1 1.0 O4 A:GAL1101 4.5 73.6 0.7 CD1 A:PHE581 4.5 53.7 1.0 CE2 A:TRP548 4.6 28.2 1.0 OE1 A:GLU549 4.6 29.3 1.0 CB A:ASP207 4.6 52.9 1.0 NE2 A:HIS520 4.7 30.3 1.0 CD1 A:TRP548 4.7 29.6 1.0 CZ2 A:TRP548 4.7 28.3 1.0 C3 A:GAL1101 4.7 55.4 0.7 C A:VAL582 4.7 45.2 1.0 O A:ASP207 4.9 39.2 1.0

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


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 in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1116 b:53.3 occ:1.00 O A:THR583 2.8 41.7 1.0 O A:HOH1479 2.8 41.4 1.0 OD2 A:ASP766 2.8 39.2 1.0 O A:HOH1317 3.0 38.4 1.0 N A:GLY523 3.2 33.7 1.0 CA A:GLY523 3.4 31.7 1.0 O A:HOH1324 3.6 37.8 1.0 OG1 A:THR583 3.6 51.1 1.0 C A:THR583 3.9 50.0 1.0 CG A:ASP766 4.0 30.9 1.0 CG A:MET522 4.1 31.5 1.0 ND2 A:ASN580 4.2 40.2 1.0 C A:MET522 4.2 29.8 1.0 NE2 A:GLN915 4.4 32.0 1.0 CB A:THR583 4.4 32.1 1.0 OE2 A:GLU552 4.5 35.4 1.0 CA A:MET522 4.6 30.4 1.0 OD1 A:ASP766 4.6 31.2 1.0 CA A:THR583 4.8 45.2 1.0 CD1 A:TYR911 4.8 33.5 1.0 N A:ASP584 4.8 55.6 1.0 O A:ASN580 4.8 56.5 1.0 C A:GLY523 4.9 34.1 1.0 CA A:ASP584 4.9 42.7 1.0 CB A:MET522 5.0 37.0 1.0 CE A:MET522 5.0 42.2 1.0

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


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 in Complex with Galactose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1117 b:51.1 occ:1.00 OG A:SER72 2.6 54.6 1.0 O A:HOH1222 2.8 42.0 1.0 ND2 A:ASN126 3.0 37.2 1.0 CB A:SER72 3.3 43.5 1.0 CB A:ASN126 3.4 38.1 1.0 N A:SER72 3.5 43.8 1.0 CD1 A:LEU35 3.6 58.6 1.0 CG A:ASN126 3.6 37.4 1.0 O A:HOH1403 3.9 57.9 1.0 CG2 A:VAL122 4.0 49.8 1.0 CA A:SER72 4.0 46.9 1.0 CG1 A:ILE32 4.2 51.2 1.0 O A:PRO123 4.2 40.3 1.0 CD1 A:ILE128 4.3 39.6 1.0 O A:ASN126 4.5 39.5 1.0 C A:GLY71 4.6 43.3 1.0 CA A:ASN126 4.7 38.3 1.0 CA A:GLY71 4.7 42.9 1.0 OD1 A:ASN126 4.8 38.5 1.0 CD1 A:ILE32 4.9 67.2 1.0

M.Rutkiewicz, A.Bujacz, M.Wanarska, A.Wierzbicka-Wos, H.Cieslinski. Active Site Architecture and Reaction Mechanism Determination of Cold Adapted Beta-D-Galactosidase Fromarthrobactersp. 32CB. Int J Mol Sci V. 20 2019.
ISSN: ESSN 1422-0067
PubMed: 31484304
DOI: 10.3390/IJMS20174301