Sodium in PDB 5uj6: Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase

The structure of Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase, PDB code: 5uj6 was solved by W.G.Walton, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.62 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.728, 142.943, 181.686, 90.00, 90.00, 90.00
R / Rfree (%)	14.4 / 18

The structure of Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase also contains other interesting chemical elements:

Calcium

(Ca)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase (pdb code 5uj6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase, PDB code: 5uj6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na905 b:18.0 occ:1.00 HG1 A:THR776 1.9 31.7 1.0 O A:ASN878 2.4 20.2 1.0 O A:LEU773 2.5 22.2 1.0 OD1 A:ASN724 2.5 22.8 1.0 O A:VAL725 2.6 20.1 1.0 O A:THR776 2.6 20.6 1.0 OG1 A:THR776 2.7 26.4 1.0 C A:THR776 3.3 22.3 1.0 C A:ASN878 3.5 18.6 1.0 HD12 A:LEU773 3.5 29.1 1.0 C A:LEU773 3.6 19.9 1.0 H A:THR776 3.6 23.2 1.0 H A:VAL725 3.6 26.1 1.0 HA A:ASN878 3.6 22.3 1.0 C A:VAL725 3.6 20.1 1.0 N A:VAL725 3.6 21.8 1.0 CG A:ASN724 3.6 19.7 1.0 CB A:THR776 3.7 25.1 1.0 HA A:ASN724 3.7 23.4 1.0 HB3 A:ASN878 3.7 24.1 1.0 HA A:LEU773 3.8 26.6 1.0 C A:ASN724 3.8 20.3 1.0 HA A:LEU777 3.9 26.2 1.0 HB A:THR776 3.9 30.2 1.0 CA A:THR776 3.9 18.1 1.0 CA A:ASN878 4.0 18.6 1.0 HB2 A:SER727 4.1 27.6 1.0 CA A:VAL725 4.2 25.3 1.0 CA A:ASN724 4.2 19.5 1.0 N A:THR776 4.2 19.3 1.0 N A:LEU777 4.2 23.6 1.0 HB A:VAL725 4.2 27.7 1.0 CA A:LEU773 4.3 22.2 1.0 O A:ASN724 4.3 22.2 1.0 CB A:ASN878 4.4 20.1 1.0 CD1 A:LEU773 4.4 24.2 1.0 HA A:PHE774 4.5 23.4 1.0 HD21 A:ASN724 4.5 25.1 1.0 CB A:ASN724 4.5 18.5 1.0 CA A:LEU777 4.5 21.9 1.0 ND2 A:ASN724 4.5 20.9 1.0 HG A:LEU773 4.6 30.5 1.0 HB3 A:SER727 4.6 27.6 1.0 HA2 A:GLY879 4.6 20.7 1.0 N A:GLY879 4.6 18.4 1.0 N A:PHE774 4.7 20.2 1.0 O A:PRO772 4.7 19.5 1.0 HD11 A:LEU773 4.7 29.1 1.0 N A:GLY726 4.7 24.3 1.0 HA3 A:GLY726 4.7 33.7 1.0 CB A:VAL725 4.8 23.1 1.0 CB A:SER727 4.8 23.0 1.0 HA A:THR776 4.9 21.7 1.0 H A:LEU777 4.9 28.3 1.0 O A:HOH1309 4.9 27.7 1.0 H A:SER727 4.9 27.4 1.0 HA3 A:GLY879 4.9 20.7 1.0 CG A:LEU773 4.9 25.4 1.0 CA A:PHE774 4.9 19.5 1.0 HB2 A:ASN878 4.9 24.1 1.0 CA A:GLY879 5.0 17.2 1.0 HB3 A:LEU777 5.0 25.5 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na905 b:16.4 occ:1.00 OD1 B:ASN724 2.4 21.5 1.0 O B:ASN878 2.4 19.7 1.0 O B:LEU773 2.5 22.5 1.0 OG1 B:THR776 2.6 22.7 1.0 O B:THR776 2.6 21.3 1.0 O B:VAL725 2.6 20.7 1.0 C B:THR776 3.3 23.4 1.0 HD12 B:LEU773 3.4 22.2 1.0 C B:ASN878 3.5 19.4 1.0 H B:THR776 3.6 24.5 1.0 CG B:ASN724 3.6 18.9 1.0 C B:LEU773 3.6 22.8 1.0 CB B:THR776 3.6 25.5 1.0 C B:VAL725 3.7 23.1 1.0 HA B:ASN724 3.7 19.7 1.0 HA B:ASN878 3.7 21.7 1.0 HA B:LEU773 3.7 26.2 1.0 N B:VAL725 3.7 22.4 1.0 H B:VAL725 3.8 26.8 1.0 HB B:THR776 3.8 30.6 1.0 C B:ASN724 3.8 20.8 1.0 HB3 B:ASN878 3.8 22.4 1.0 CA B:THR776 3.9 19.2 1.0 HA B:LEU777 3.9 23.0 1.0 CA B:ASN878 4.1 18.1 1.0 HB2 B:SER727 4.1 30.8 1.0 N B:THR776 4.1 20.4 1.0 CA B:ASN724 4.1 16.4 1.0 O B:ASN724 4.2 20.6 1.0 CA B:VAL725 4.2 19.1 1.0 CA B:LEU773 4.2 21.8 1.0 N B:LEU777 4.2 25.7 1.0 HB B:VAL725 4.3 26.2 1.0 CD1 B:LEU773 4.3 18.5 1.0 HD21 B:ASN724 4.5 24.4 1.0 HB3 B:SER727 4.5 30.8 1.0 CB B:ASN724 4.5 17.7 1.0 CB B:ASN878 4.5 18.6 1.0 HG B:LEU773 4.5 29.6 1.0 HA B:PHE774 4.5 24.9 1.0 ND2 B:ASN724 4.5 20.3 1.0 HD11 B:LEU773 4.5 22.2 1.0 CA B:LEU777 4.6 19.2 1.0 HA3 B:GLY726 4.6 23.1 1.0 O B:PRO772 4.6 21.6 1.0 N B:GLY879 4.7 17.1 1.0 HA2 B:GLY879 4.7 21.5 1.0 N B:PHE774 4.7 20.8 1.0 N B:GLY726 4.7 21.5 1.0 CB B:SER727 4.7 25.7 1.0 O B:HOH1499 4.8 26.7 1.0 HA B:THR776 4.8 23.0 1.0 CB B:VAL725 4.8 21.9 1.0 CG B:LEU773 4.9 24.6 1.0 H B:SER727 4.9 27.5 1.0 H B:LEU777 4.9 30.9 1.0 CG2 B:THR776 5.0 22.2 1.0 CA B:PHE774 5.0 20.7 1.0 HD22 B:ASN878 5.0 26.5 1.0 HD13 B:LEU773 5.0 22.2 1.0 N B:SER727 5.0 22.9 1.0

R.M.Pollet, E.H.D'agostino, W.G.Walton, Y.Xu, M.S.Little, K.A.Biernat, S.J.Pellock, L.M.Patterson, B.C.Creekmore, H.N.Isenberg, R.R.Bahethi, A.P.Bhatt, J.Liu, R.Z.Gharaibeh, M.R.Redinbo. An Atlas of Beta-Glucuronidases in the Human Intestinal Microbiome. Structure V. 25 967 2017.
ISSN: ISSN 1878-4186
PubMed: 28578872
DOI: 10.1016/J.STR.2017.05.003