Sodium in PDB 7lj2: Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose

The structure of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose, PDB code: 7lj2 was solved by C.S.Robb, A.B.Boraston, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.79 / 2.40
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	89.67, 89.67, 267.06, 90, 90, 90
R / Rfree (%)	18.2 / 23.1

The structure of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose (pdb code 7lj2). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose, PDB code: 7lj2:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose within 5.0Å range: probe atom residue distance (Å) B Occ A:Na602 b:21.8 occ:1.00 OG A:SER179 2.8 31.6 1.0 OG A:SER180 3.0 29.4 1.0 N A:LYS208 3.2 31.8 1.0 N A:SER180 3.2 24.8 1.0 CA A:SER180 3.4 26.6 1.0 N A:ALA209 3.4 28.6 1.0 C A:SER179 3.6 27.8 1.0 CB A:LYS208 3.7 34.6 1.0 CD1 A:ILE183 3.7 27.7 1.0 CB A:SER179 3.7 31.9 1.0 CB A:SER180 3.7 30.1 1.0 CA A:LYS208 3.8 31.6 1.0 CD1 A:TYR207 3.9 28.7 1.0 O A:SER179 3.9 31.2 1.0 C A:LYS208 4.1 32.2 1.0 C A:TYR207 4.2 32.3 1.0 CB A:ALA209 4.2 25.1 1.0 CB A:TYR207 4.2 34.1 1.0 CA A:TYR207 4.2 28.2 1.0 CA A:SER179 4.3 28.7 1.0 CA A:ALA209 4.4 33.2 1.0 CG A:TYR207 4.5 31.3 1.0 CG A:LYS208 4.7 39.8 1.0 CG1 A:ILE183 4.8 26.7 1.0 C A:SER180 4.8 29.6 1.0 CE1 A:TYR207 4.9 30.1 1.0 CD A:LYS208 5.0 36.0 1.0

Sodium binding site 2 out of 2 in the Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Exo-L-Galactose-6-Sulfatase BUS1_11 From Bacteroides Uniformis in Complex with Neoporphyrabiose within 5.0Å range: probe atom residue distance (Å) B Occ B:Na602 b:15.6 occ:1.00 OG B:SER180 2.9 23.9 1.0 OG B:SER179 3.1 29.0 1.0 N B:LYS208 3.1 26.1 1.0 N B:ALA209 3.3 29.7 1.0 N B:SER180 3.4 24.3 1.0 CA B:SER180 3.5 25.2 1.0 CB B:LYS208 3.7 33.2 1.0 C B:SER179 3.7 26.9 1.0 CB B:SER179 3.7 28.4 1.0 CA B:LYS208 3.7 27.8 1.0 CB B:SER180 3.8 24.5 1.0 CD1 B:TYR207 3.8 29.4 1.0 CD1 B:ILE183 3.9 27.0 1.0 C B:LYS208 3.9 28.5 1.0 CB B:TYR207 4.0 28.3 1.0 CB B:ALA209 4.0 25.9 1.0 C B:TYR207 4.1 30.1 1.0 O B:SER179 4.1 26.7 1.0 CA B:TYR207 4.1 29.4 1.0 CG B:LYS208 4.2 40.5 1.0 CA B:ALA209 4.2 28.1 1.0 CA B:SER179 4.3 27.8 1.0 CG B:TYR207 4.4 28.9 1.0 CE1 B:TYR207 4.9 26.1 1.0 C B:SER180 4.9 24.1 1.0 CD B:LYS208 5.0 38.1 1.0

C.S.Robb, J.K.Hobbs, B.Pluvinage, G.Reintjes, L.Klassen, S.Monteith, G.Giljan, C.Amundsen, C.Vickers, A.G.Hettle, R.Hills, X.Xing, T.Montina, W.F.Zandberg, D.W.Abbott, A.B.Boraston. Metabolism of A Hybrid Algal Galactan By Members of the Human Gut Microbiome. Nat.Chem.Biol. V. 18 501 2022.
ISSN: ESSN 1552-4469
PubMed: 35289327
DOI: 10.1038/S41589-022-00983-Y