Sodium in PDB 6sec: Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CBON Complex with Onpg

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

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CBON Complex with Onpg, PDB code: 6sec 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)	46.58 / 2.77
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.330, 137.330, 126.784, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 24

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CBON Complex with Onpg (pdb code 6sec). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CBON Complex with Onpg, PDB code: 6sec:

Sodium binding site 1 out of 1 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CBON Complex with Onpg


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. 32CBON Complex with Onpg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1103 b:59.1 occ:1.00 OD2 A:ASP584 2.3 52.3 1.0 OD2 A:ASP207 2.5 68.1 1.0 O A:PHE581 2.5 62.7 1.0 O A:HOH1298 2.7 42.4 1.0 O6 A:1451104 2.8 73.2 1.0 CG A:ASP584 3.3 52.5 1.0 CD2 A:PHE581 3.4 63.3 1.0 CG A:ASP207 3.5 70.5 1.0 C6 A:1451104 3.6 77.3 1.0 C A:PHE581 3.6 67.6 1.0 OD1 A:ASP207 3.8 73.4 1.0 NE1 A:TRP548 4.0 55.1 1.0 CE2 A:PHE581 4.0 68.1 1.0 OD1 A:ASP584 4.0 54.7 1.0 OH A:TYR108 4.1 59.9 1.0 O4 A:1451104 4.2 63.6 1.0 CG A:PHE581 4.3 64.0 1.0 CB A:ASP584 4.3 45.2 1.0 CB A:PHE581 4.4 45.0 1.0 N A:VAL582 4.5 78.7 1.0 CA A:PHE581 4.5 57.1 1.0 NE2 A:HIS520 4.5 45.5 1.0 CA A:VAL582 4.5 79.0 1.0 C4 A:1451104 4.7 77.3 1.0 C5 A:1451104 4.7 80.0 1.0 ND2 A:ASN110 4.7 61.6 1.0 OE2 A:GLU549 4.7 44.6 1.0 CB A:ASP207 4.8 70.1 1.0 CD1 A:TRP548 4.8 46.7 1.0 CE2 A:TRP548 4.9 60.4 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