Sodium in PDB 6d8g: D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2

The structure of D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2, PDB code: 6d8g 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)	29.55 / 3.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.990, 142.018, 181.239, 90.00, 90.00, 90.00
R / Rfree (%)	16.6 / 24.1

The binding sites of Sodium atom in the D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2 (pdb code 6d8g). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2, PDB code: 6d8g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na901 b:39.4 occ:1.00 O A:THR776 2.3 55.3 1.0 O A:ASN878 2.5 52.5 1.0 OD1 A:ASN724 2.5 50.1 1.0 O A:VAL725 2.6 56.1 1.0 O A:LEU773 2.6 51.7 1.0 OG1 A:THR776 3.0 58.9 1.0 C A:THR776 3.2 56.4 1.0 N A:VAL725 3.6 50.0 1.0 C A:ASN878 3.6 52.9 1.0 C A:VAL725 3.6 48.6 1.0 CG A:ASN724 3.7 49.3 1.0 C A:LEU773 3.8 48.0 1.0 C A:ASN724 3.9 46.8 1.0 CB A:THR776 3.9 57.1 1.0 CA A:THR776 4.0 55.6 1.0 CA A:ASN878 4.0 53.5 1.0 CA A:VAL725 4.1 50.0 1.0 N A:THR776 4.1 53.8 1.0 N A:LEU777 4.2 59.6 1.0 CD1 A:LEU773 4.2 42.6 1.0 CA A:ASN724 4.2 42.1 1.0 CB A:ASN878 4.3 53.6 1.0 CA A:LEU777 4.4 60.4 1.0 O A:ASN724 4.5 51.6 1.0 CA A:LEU773 4.5 41.5 1.0 CB A:ASN724 4.6 46.3 1.0 ND2 A:ASN724 4.6 50.2 1.0 N A:SER727 4.7 55.2 1.0 CB A:SER727 4.7 55.8 1.0 CB A:VAL725 4.7 50.1 1.0 N A:GLY726 4.7 52.9 1.0 N A:GLY879 4.8 43.8 1.0 O A:PRO772 4.8 50.8 1.0 N A:PHE774 4.9 51.0 1.0 CG A:LEU773 4.9 43.3 1.0

Sodium binding site 2 out of 2 in the D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of D341A D367A Calcium Binding Mutant of Bacteroides Uniformis Beta- Glucuronidase 2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na901 b:39.9 occ:1.00 O B:THR776 2.3 58.5 1.0 O B:ASN878 2.4 54.4 1.0 O B:LEU773 2.5 48.3 1.0 OD1 B:ASN724 2.5 58.6 1.0 O B:VAL725 2.9 55.8 1.0 C B:THR776 3.4 57.3 1.0 OG1 B:THR776 3.4 56.6 1.0 C B:ASN878 3.6 51.2 1.0 C B:LEU773 3.6 53.8 1.0 CG B:ASN724 3.7 55.9 1.0 N B:VAL725 3.7 54.8 1.0 C B:ASN724 3.9 54.7 1.0 C B:VAL725 3.9 56.2 1.0 CA B:THR776 4.1 57.4 1.0 CA B:ASN878 4.1 52.3 1.0 N B:THR776 4.1 56.5 1.0 CB B:THR776 4.1 58.3 1.0 CA B:ASN724 4.2 53.2 1.0 O B:ASN724 4.2 55.1 1.0 CA B:LEU773 4.3 53.0 1.0 CA B:VAL725 4.3 58.4 1.0 N B:LEU777 4.4 58.5 1.0 CD1 B:LEU773 4.4 47.3 1.0 CB B:ASN878 4.5 52.7 1.0 CB B:ASN724 4.6 53.7 1.0 ND2 B:ASN724 4.6 51.5 1.0 CG B:LEU773 4.6 51.8 1.0 CA B:LEU777 4.6 60.3 1.0 N B:GLY879 4.7 46.8 1.0 N B:PHE774 4.7 53.0 1.0 CB B:SER727 4.7 59.8 1.0 O B:PRO772 4.8 50.3 1.0 CB B:VAL725 4.9 57.8 1.0 CA B:GLY879 4.9 48.8 1.0 CA B:PHE774 5.0 53.9 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