Sodium in PDB 6d50: Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone

The structure of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone, PDB code: 6d50 was solved by W.G.Walton, S.J.Pellock, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.48 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.489, 141.880, 180.803, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 23.1

The structure of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone (pdb code 6d50). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone, PDB code: 6d50:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone within 5.0Å range: probe atom residue distance (Å) B Occ A:Na902 b:25.7 occ:1.00 O A:VAL725 2.4 36.1 1.0 O A:ASN878 2.5 36.3 1.0 OD1 A:ASN724 2.5 32.1 1.0 O A:THR776 2.6 38.6 1.0 O A:LEU773 2.7 33.4 1.0 OG1 A:THR776 2.8 36.8 1.0 C A:THR776 3.3 38.4 1.0 C A:VAL725 3.4 40.4 1.0 N A:VAL725 3.4 34.1 1.0 C A:ASN878 3.6 36.1 1.0 C A:ASN724 3.6 32.4 1.0 CG A:ASN724 3.7 32.0 1.0 C A:LEU773 3.8 33.4 1.0 CB A:THR776 3.9 39.4 1.0 CA A:VAL725 3.9 38.5 1.0 O A:ASN724 4.0 38.5 1.0 CA A:THR776 4.0 32.7 1.0 N A:LEU777 4.1 35.4 1.0 CA A:ASN724 4.1 32.6 1.0 CA A:ASN878 4.2 33.1 1.0 N A:THR776 4.2 36.7 1.0 CD1 A:LEU773 4.4 33.2 1.0 CA A:LEU777 4.4 34.8 1.0 N A:GLY726 4.5 39.4 1.0 CB A:ASN724 4.5 32.2 1.0 ND2 A:ASN724 4.5 35.3 1.0 CB A:ASN878 4.6 32.0 1.0 CB A:VAL725 4.6 34.5 1.0 CA A:LEU773 4.6 31.7 1.0 CB A:SER727 4.7 38.0 1.0 N A:GLY879 4.7 36.1 1.0 O A:PRO772 4.8 34.9 1.0 CA A:GLY726 4.8 40.2 1.0 N A:PHE774 4.8 32.3 1.0 O A:HOH1168 4.9 33.6 1.0 CA A:GLY879 4.9 30.7 1.0

Sodium binding site 2 out of 2 in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone within 5.0Å range: probe atom residue distance (Å) B Occ B:Na902 b:26.8 occ:1.00 OD1 B:ASN724 2.4 39.9 1.0 O B:THR776 2.5 37.5 1.0 O B:ASN878 2.6 41.5 1.0 O B:VAL725 2.6 38.9 1.0 O B:LEU773 2.6 37.9 1.0 OG1 B:THR776 2.6 34.8 1.0 C B:THR776 3.3 40.8 1.0 CG B:ASN724 3.5 35.6 1.0 C B:VAL725 3.6 35.9 1.0 CB B:THR776 3.6 42.0 1.0 N B:VAL725 3.6 41.8 1.0 C B:ASN878 3.7 41.4 1.0 C B:LEU773 3.7 36.2 1.0 C B:ASN724 3.7 39.0 1.0 CA B:THR776 3.9 35.9 1.0 O B:ASN724 4.0 36.6 1.0 N B:THR776 4.1 26.4 1.0 CA B:ASN724 4.1 35.5 1.0 CA B:VAL725 4.2 38.4 1.0 CA B:ASN878 4.2 35.3 1.0 N B:LEU777 4.3 43.0 1.0 CA B:LEU773 4.3 33.5 1.0 CD1 B:LEU773 4.4 32.9 1.0 ND2 B:ASN724 4.4 32.6 1.0 CB B:ASN878 4.4 34.6 1.0 CB B:ASN724 4.5 34.5 1.0 CB B:SER727 4.6 34.6 1.0 CA B:LEU777 4.7 46.0 1.0 N B:GLY726 4.7 37.7 1.0 O B:PRO772 4.7 38.0 1.0 O B:HOH1186 4.8 27.2 1.0 N B:PHE774 4.8 37.7 1.0 CB B:VAL725 4.8 35.6 1.0 N B:GLY879 4.8 38.4 1.0 N B:SER727 4.9 40.5 1.0 CG B:LEU773 5.0 32.2 1.0

S.J.Pellock, W.G.Walton, K.A.Biernat, D.Torres-Rivera, B.C.Creekmore, Y.Xu, J.Liu, A.Tripathy, L.J.Stewart, M.R.Redinbo. Three Structurally and Functionally Distinct Beta-Glucuronidases From the Human Gut Microbebacteroides Uniformis. J. Biol. Chem. V. 293 18559 2018.
ISSN: ESSN 1083-351X
PubMed: 30301767
DOI: 10.1074/JBC.RA118.005414