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

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

The structure of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg, PDB code: 6seb 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)	46.54 / 2.27
Space group	P 31 2 1
Cell size a, b, c (Å), α, β, γ (°)	137.069, 137.069, 126.795, 90.00, 90.00, 120.00
R / Rfree (%)	15.7 / 20.5

The binding sites of Sodium atom in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg (pdb code 6seb). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg, PDB code: 6seb:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg


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 Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1108 b:45.2 occ:1.00 OD2 A:ASP584 2.4 38.8 1.0 OD1 A:ASP207 2.4 42.3 1.0 O A:HOH1662 2.5 35.8 1.0 O A:PHE581 2.5 44.5 1.0 O6 A:IPT1101 2.6 52.8 0.7 CG A:ASP207 3.3 44.0 1.0 CG A:ASP584 3.4 43.5 1.0 C6 A:IPT1101 3.4 55.8 0.7 OD2 A:ASP207 3.4 44.4 1.0 C A:PHE581 3.6 49.1 1.0 OH A:TYR108 3.8 40.9 0.5 OH A:TYR108 3.8 40.9 0.5 NE1 A:TRP548 3.9 36.4 1.0 OD1 A:ASP584 4.0 40.2 1.0 O4 A:IPT1101 4.2 41.2 0.7 CA A:VAL582 4.3 48.3 1.0 N A:VAL582 4.3 49.0 1.0 CB A:PHE581 4.4 45.5 1.0 OE2 A:GLU549 4.4 32.1 1.0 CB A:ASP584 4.5 33.4 1.0 CA A:PHE581 4.5 45.1 1.0 CD2 A:PHE581 4.6 43.0 1.0 CB A:ASP207 4.7 34.1 1.0 C5 A:IPT1101 4.7 58.4 0.7 NE2 A:HIS520 4.7 28.1 1.0 CE2 A:TRP548 4.8 33.6 1.0 CD1 A:TRP548 4.8 25.0 1.0 C4 A:IPT1101 4.8 53.8 0.7 O A:ASP207 4.9 33.7 1.0 CZ2 A:TRP548 4.9 27.3 1.0 CZ A:TYR108 4.9 42.2 0.5 CZ A:TYR108 4.9 42.2 0.5 C A:VAL582 5.0 43.7 1.0

Sodium binding site 2 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg


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 Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1109 b:47.7 occ:1.00 O A:HOH1283 2.8 35.2 1.0 N A:VAL519 3.0 32.9 1.0 OH A:TYR532 3.0 33.0 1.0 CB A:TYR518 3.4 25.0 1.0 CA A:TYR518 3.4 28.2 1.0 CA A:TYR482 3.6 36.4 1.0 CZ A:TYR532 3.6 40.9 1.0 C A:TYR518 3.7 32.5 1.0 CA A:VAL519 3.8 28.1 1.0 CD A:PRO987 3.8 36.4 1.0 CE2 A:TYR532 3.8 35.8 1.0 CD1 A:TYR482 3.9 30.6 1.0 CB A:TYR482 4.1 33.5 1.0 C A:TYR482 4.2 40.5 1.0 O A:ALA483 4.4 37.7 1.0 O A:TYR482 4.4 38.0 1.0 CG A:TYR518 4.4 29.5 1.0 CG A:TYR482 4.5 32.1 1.0 CG A:PRO987 4.5 39.5 1.0 N A:TYR482 4.5 39.0 1.0 CD2 A:TYR518 4.6 32.9 1.0 CG1 A:VAL519 4.6 33.4 1.0 CE1 A:TYR532 4.6 31.7 1.0 N A:HIS520 4.7 24.5 1.0 OG1 A:THR982 4.7 30.4 1.0 C A:VAL519 4.8 33.0 1.0 N A:TYR518 4.8 34.0 1.0 CB A:VAL519 4.9 28.0 1.0 CE1 A:TYR482 4.9 34.2 1.0 O A:TYR518 4.9 34.7 1.0 O A:HOH1435 4.9 33.4 1.0 CD2 A:TYR532 4.9 33.6 1.0 N A:ALA483 5.0 34.3 1.0 O A:GLU517 5.0 28.4 1.0

Sodium binding site 3 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg


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 Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1110 b:50.8 occ:1.00 OE1 A:GLN951 2.7 41.6 1.0 N A:ALA763 2.9 35.3 1.0 OE1 A:GLU916 2.9 42.5 1.0 CB A:ALA763 3.3 35.7 1.0 CD A:GLN951 3.4 45.3 1.0 CD2 A:LEU954 3.5 32.7 1.0 CG A:GLN951 3.5 41.8 1.0 CA A:TRP762 3.7 38.3 1.0 CB A:TRP762 3.7 37.2 1.0 CA A:ALA763 3.7 38.4 1.0 C A:TRP762 3.7 41.1 1.0 NH1 A:ARG947 3.7 42.3 1.0 O A:HOH1610 3.8 38.0 1.0 CB A:GLU916 3.9 28.3 1.0 NH2 A:ARG947 4.0 41.7 1.0 CD A:GLU916 4.0 42.1 1.0 CB A:GLN951 4.1 41.4 1.0 CA A:GLU916 4.2 32.7 1.0 CZ A:ARG947 4.2 49.3 1.0 O A:ALA763 4.5 39.9 1.0 NH2 A:ARG863 4.6 29.4 1.0 CG A:GLU916 4.6 31.4 1.0 CG A:LEU954 4.6 43.9 1.0 CA A:GLN951 4.6 42.6 1.0 C A:ALA763 4.6 37.9 1.0 NE2 A:GLN951 4.7 43.6 1.0 N A:GLU916 4.7 37.9 1.0 CG A:TRP762 4.8 47.3 1.0 O A:TRP762 4.9 36.1 1.0

Sodium binding site 4 out of 4 in the Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cold-Adapted Beta-D-Galactosidase From Arthrobacter Sp. 32CB in Complex with Iptg within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1111 b:56.4 occ:1.00 N A:VAL946 2.9 45.2 1.0 O A:GLY918 2.9 44.9 1.0 O A:HOH1309 3.0 41.9 1.0 CG2 A:THR945 3.1 33.0 1.0 O A:VAL946 3.3 48.6 1.0 CA A:THR945 3.4 41.6 1.0 C A:THR945 3.6 45.9 1.0 CB A:MET907 3.7 42.1 1.0 C A:GLY918 3.7 43.7 1.0 CE A:MET907 3.8 37.9 1.0 CB A:THR945 3.9 45.6 1.0 O A:MET907 3.9 42.0 1.0 C A:VAL946 4.0 46.0 1.0 CA A:VAL946 4.0 45.5 1.0 NH1 A:ARG920 4.2 46.8 1.0 CA A:GLY918 4.2 34.9 1.0 O A:LEU944 4.4 40.3 1.0 C A:MET907 4.4 42.3 1.0 O A:HOH1503 4.4 41.7 1.0 CG A:MET907 4.5 41.3 1.0 N A:THR945 4.6 41.7 1.0 CA A:MET907 4.6 47.3 1.0 CB A:VAL946 4.6 43.0 1.0 N A:ALA919 4.7 44.3 1.0 OG1 A:THR945 4.7 45.0 1.0 O A:THR945 4.9 42.4 1.0 C A:LEU944 4.9 43.5 1.0 SD A:MET907 4.9 50.9 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