Sodium in PDB 6se9: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Shallow Mode

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

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Shallow Mode, PDB code: 6se9 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)	47.04 / 1.97
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	138.902, 138.902, 127.875, 90.00, 90.00, 120.00
R / Rfree (%)	20.2 / 23.8

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB Mutant E441Q in Complex with Lactose Bound in Shallow Mode (pdb code 6se9). 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 Lactose Bound in Shallow Mode, PDB code: 6se9:
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 Lactose Bound in Shallow Mode


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 Lactose Bound in Shallow Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1101 b:59.9 occ:1.00 O A:PHE581 2.4 64.1 1.0 OD2 A:ASP207 2.4 50.8 1.0 O A:HOH1407 2.5 55.9 1.0 OD2 A:ASP584 2.5 53.5 1.0 O6 A:LAT1103 2.6 77.6 1.0 CG A:ASP207 3.3 52.2 1.0 CG A:ASP584 3.4 54.6 1.0 C A:PHE581 3.4 63.7 1.0 C6 A:LAT1103 3.5 79.6 1.0 OD1 A:ASP207 3.6 53.9 1.0 OH A:TYR108 3.7 55.9 1.0 NE1 A:TRP548 4.0 51.1 1.0 OD1 A:ASP584 4.0 54.4 1.0 O4 A:LAT1103 4.1 80.2 1.0 CA A:VAL582 4.1 62.5 1.0 N A:VAL582 4.2 62.7 1.0 OE2 A:GLU549 4.3 53.4 1.0 CB A:PHE581 4.4 64.2 1.0 C4 A:LAT1103 4.4 82.3 1.0 CA A:PHE581 4.4 64.0 1.0 CB A:ASP584 4.4 54.7 1.0 CB A:ASP207 4.5 46.8 1.0 C5 A:LAT1103 4.6 82.2 1.0 O A:ASP207 4.8 46.9 1.0 CZ A:TYR108 4.8 58.5 1.0 CE2 A:TRP548 4.8 50.9 1.0 C A:VAL582 4.8 61.9 1.0 NE2 A:HIS520 4.8 53.0 1.0 CZ2 A:TRP548 4.9 51.6 1.0 CD2 A:PHE581 4.9 65.7 1.0 CD1 A:TRP548 4.9 50.5 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 Lactose Bound in Shallow Mode


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 Lactose Bound in Shallow Mode within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1102 b:62.9 occ:1.00 O A:HOH1428 2.5 57.5 1.0 O A:HOH1304 2.8 54.9 1.0 O A:THR583 2.8 58.4 1.0 OD2 A:ASP766 2.9 56.0 1.0 N A:GLY523 3.4 53.6 1.0 OG1 A:THR583 3.7 64.6 1.0 CA A:GLY523 3.7 58.6 1.0 O A:HOH1378 3.7 52.4 1.0 ND2 A:ASN580 4.0 60.9 1.0 C A:THR583 4.0 59.6 1.0 CG A:ASP766 4.0 56.0 1.0 CG A:MET522 4.0 53.8 1.0 CB A:THR583 4.3 64.6 1.0 NE2 A:GLN915 4.3 55.3 1.0 C A:MET522 4.4 52.7 1.0 OE2 A:GLU552 4.4 60.2 1.0 OD1 A:ASP766 4.6 57.1 1.0 CA A:MET522 4.7 53.4 1.0 O A:ASN580 4.7 61.1 1.0 CA A:THR583 4.8 62.1 1.0 CE A:MET522 4.8 54.6 1.0 CD1 A:TYR911 4.9 58.1 1.0 N A:ASP584 4.9 56.2 1.0 CB A:TYR911 5.0 59.7 1.0 CB A:MET522 5.0 53.4 1.0 CG A:ASN580 5.0 60.8 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