Sodium in PDB 6ed1: Bacteroides Dorei Beta-Glucuronidase

The structure of Bacteroides Dorei Beta-Glucuronidase, PDB code: 6ed1 was solved by K.A.Biernat, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.54 / 2.90
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	242.663, 101.355, 168.600, 90.00, 94.97, 90.00
R / Rfree (%)	17.8 / 26.8

The binding sites of Sodium atom in the Bacteroides Dorei Beta-Glucuronidase (pdb code 6ed1). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Bacteroides Dorei Beta-Glucuronidase, PDB code: 6ed1:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Bacteroides Dorei Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:27.3 occ:1.00 OG1 A:THR770 2.3 22.5 1.0 O A:LEU705 2.3 21.8 1.0 O A:THR770 2.4 22.2 1.0 OD1 A:ASN704 2.4 23.9 1.0 O A:LEU767 2.5 17.8 1.0 O A:SER871 2.5 26.6 1.0 C A:THR770 3.0 22.2 1.0 C A:SER871 3.3 23.4 1.0 C A:LEU705 3.4 24.6 1.0 CB A:THR770 3.4 24.2 1.0 CA A:SER871 3.5 21.6 1.0 N A:LEU705 3.6 25.1 1.0 CG A:ASN704 3.6 23.8 1.0 C A:LEU767 3.7 18.9 1.0 CA A:THR770 3.8 19.4 1.0 N A:PHE771 3.8 18.3 1.0 CB A:SER871 3.8 23.4 1.0 C A:ASN704 4.0 25.4 1.0 CD1 A:LEU767 4.0 23.7 1.0 CA A:LEU705 4.0 29.3 1.0 CA A:PHE771 4.1 21.1 1.0 N A:THR770 4.3 17.3 1.0 CA A:ASN704 4.3 21.3 1.0 CA A:LEU767 4.4 19.9 1.0 N A:GLY706 4.5 28.0 1.0 N A:GLY872 4.5 22.1 1.0 ND2 A:ASN704 4.5 21.3 1.0 OG A:SER871 4.5 21.4 1.0 O A:ASN704 4.5 31.5 1.0 CB A:ASN704 4.6 24.5 1.0 CB A:LEU705 4.6 35.0 1.0 O A:PHE768 4.7 17.4 1.0 N A:PHE768 4.7 20.2 1.0 CG2 A:THR770 4.7 26.3 1.0 CA A:GLY706 4.8 29.6 1.0 C A:PHE768 4.8 18.7 1.0 CB A:PHE771 4.8 20.9 1.0 CA A:PHE768 4.9 20.4 1.0 O A:PRO766 4.9 19.9 1.0 N A:SER871 4.9 21.7 1.0 CG A:LEU767 5.0 22.7 1.0 CA A:GLY872 5.0 27.7 1.0 O A:ILE870 5.0 23.8 1.0

Sodium binding site 2 out of 4 in the Bacteroides Dorei Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:15.2 occ:1.00 OD1 B:ASN704 2.1 15.2 1.0 O B:THR770 2.3 20.0 1.0 O B:LEU705 2.4 18.2 1.0 O B:SER871 2.4 16.6 1.0 O B:LEU767 2.5 23.1 1.0 OG1 B:THR770 2.5 21.0 1.0 C B:THR770 3.1 18.3 1.0 CG B:ASN704 3.4 18.1 1.0 C B:LEU705 3.5 18.2 1.0 CD1 B:LEU767 3.5 19.0 1.0 C B:SER871 3.5 18.6 1.0 CB B:THR770 3.5 21.2 1.0 N B:LEU705 3.5 18.1 1.0 C B:LEU767 3.5 19.8 1.0 CA B:THR770 3.8 20.2 1.0 C B:ASN704 3.8 17.9 1.0 CA B:SER871 4.0 15.8 1.0 CA B:LEU767 4.0 12.5 1.0 CA B:LEU705 4.0 17.3 1.0 N B:PHE771 4.1 17.0 1.0 N B:THR770 4.1 21.9 1.0 ND2 B:ASN704 4.2 16.2 1.0 CA B:ASN704 4.2 16.5 1.0 CB B:SER871 4.2 17.7 1.0 CB B:ASN704 4.4 19.9 1.0 O B:PRO766 4.4 23.7 1.0 O B:ASN704 4.4 15.2 1.0 CA B:PHE771 4.4 17.2 1.0 CB B:LEU705 4.6 14.4 1.0 N B:GLY706 4.6 19.0 1.0 N B:GLY872 4.7 14.9 1.0 CB B:GLN707 4.7 19.1 1.0 CG B:LEU767 4.7 14.6 1.0 N B:PHE768 4.7 21.6 1.0 N B:GLN707 4.8 17.9 1.0 CG2 B:THR770 4.8 21.6 1.0 CB B:LEU767 4.9 11.3 1.0 CA B:GLY872 5.0 15.2 1.0 OG B:SER871 5.0 20.8 1.0 CA B:GLY706 5.0 25.8 1.0

Sodium binding site 3 out of 4 in the Bacteroides Dorei Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ C:Na901 b:21.2 occ:1.00 OD1 C:ASN704 2.1 20.6 1.0 O C:LEU705 2.3 18.4 1.0 O C:LEU767 2.5 21.8 1.0 OG1 C:THR770 2.5 21.6 1.0 O C:SER871 2.6 18.5 1.0 O C:THR770 2.9 16.9 1.0 CG C:ASN704 3.3 21.9 1.0 CB C:THR770 3.4 19.6 1.0 C C:THR770 3.4 16.0 1.0 C C:LEU705 3.4 23.7 1.0 C C:LEU767 3.5 22.1 1.0 C C:SER871 3.6 17.7 1.0 N C:LEU705 3.7 17.5 1.0 C C:ASN704 3.8 22.4 1.0 CD1 C:LEU767 3.8 22.2 1.0 CA C:THR770 3.8 16.1 1.0 CA C:SER871 4.0 17.1 1.0 CA C:LEU767 4.0 18.5 1.0 CA C:LEU705 4.1 20.3 1.0 CA C:ASN704 4.1 20.3 1.0 ND2 C:ASN704 4.1 20.6 1.0 N C:THR770 4.1 16.3 1.0 CB C:SER871 4.2 16.8 1.0 CB C:ASN704 4.2 17.4 1.0 O C:ASN704 4.3 21.7 1.0 N C:PHE771 4.3 14.9 1.0 CG C:LEU767 4.6 23.6 1.0 N C:GLY706 4.6 20.9 1.0 O C:PRO766 4.6 18.4 1.0 OG C:SER871 4.6 16.0 1.0 CB C:LEU705 4.6 19.4 1.0 CA C:PHE771 4.7 17.0 1.0 N C:GLY872 4.7 21.1 1.0 N C:PHE768 4.7 21.0 1.0 CG2 C:THR770 4.7 18.4 1.0 N C:GLN707 4.8 26.6 1.0 CB C:LEU767 4.9 21.5 1.0 CA C:GLY706 4.9 18.5 1.0 CB C:GLN707 5.0 20.0 1.0

Sodium binding site 4 out of 4 in the Bacteroides Dorei Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Bacteroides Dorei Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ D:Na901 b:17.9 occ:1.00 O D:SER871 2.2 19.4 1.0 OD1 D:ASN704 2.3 19.5 1.0 OG1 D:THR770 2.4 21.6 1.0 O D:LEU705 2.6 23.4 1.0 O D:LEU767 2.8 22.9 1.0 O D:THR770 3.1 21.6 1.0 N D:LEU705 3.2 22.1 1.0 C D:SER871 3.2 20.8 1.0 C D:ASN704 3.3 18.3 1.0 CB D:THR770 3.3 17.7 1.0 CG D:ASN704 3.5 22.1 1.0 C D:LEU705 3.5 21.4 1.0 CA D:ASN704 3.7 13.2 1.0 C D:THR770 3.7 21.1 1.0 O D:ASN704 3.8 21.1 1.0 C D:LEU767 3.8 20.7 1.0 CA D:LEU705 3.9 21.1 1.0 CA D:SER871 3.9 17.3 1.0 CD1 D:LEU767 3.9 16.4 1.0 CA D:THR770 4.1 17.7 1.0 CB D:ASN704 4.1 15.8 1.0 CA D:LEU767 4.1 18.8 1.0 CB D:SER871 4.2 18.7 1.0 CG D:LEU767 4.3 21.6 1.0 N D:GLY872 4.3 20.7 1.0 CB D:LEU705 4.5 17.9 1.0 CA D:GLY872 4.5 18.6 1.0 ND2 D:ASN704 4.5 21.5 1.0 CG2 D:THR770 4.5 19.2 1.0 N D:THR770 4.5 25.9 1.0 N D:PHE771 4.6 15.4 1.0 N D:GLY706 4.7 21.6 1.0 O D:PRO766 4.7 20.4 1.0 CB D:LEU767 4.9 17.1 1.0 CB D:GLN707 4.9 18.7 1.0 N D:GLN707 4.9 22.6 1.0 CA D:PHE771 5.0 17.3 1.0 N D:PHE768 5.0 19.4 1.0

K.A.Biernat, S.J.Pellock, A.P.Bhatt, M.M.Bivins, W.G.Walton, B.N.T.Tran, L.Wei, M.C.Snider, A.P.Cesmat, A.Tripathy, D.A.Erie, M.R.Redinbo. Structure, Function, and Inhibition of Drug Reactivating Human Gut Microbial Beta-Glucuronidases. Sci Rep V. 9 825 2019.
ISSN: ESSN 2045-2322
PubMed: 30696850
DOI: 10.1038/S41598-018-36069-W