Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 2 binding sites of Calcium where determined in the Bacteroides Uniforms Beta-Glucuronidase 2 Bound to D-Glucaro-1,5- Lactone, PDB code: 6d50:
Jump to Calcium binding site number: 1; 2;

Calcium 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 Calcium with other atoms in the Ca 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:Ca901 b:37.7 occ:1.00 O A:HOH1075 2.3 34.5 1.0 O A:HOH1198 2.4 32.9 1.0 OD2 A:ASP176 2.5 30.5 1.0 O A:HOH1072 2.5 40.6 1.0 OD1 A:ASP341 2.5 36.7 1.0 OD1 A:ASP367 2.7 39.7 1.0 OD2 A:ASP341 2.9 42.9 1.0 OD2 A:ASP367 3.0 33.5 1.0 CG A:ASP341 3.1 40.8 1.0 CG A:ASP367 3.2 37.1 1.0 CG A:ASP176 3.6 36.8 1.0 CB A:ASP176 4.2 36.0 1.0 NZ B:LYS854 4.3 32.1 1.0 O A:HOH1031 4.4 36.4 1.0 O A:HOH1067 4.5 30.8 1.0 CB A:ALA369 4.5 30.5 1.0 OD2 A:ASP108 4.6 44.0 1.0 N A:ASP176 4.6 38.0 1.0 CB A:ASP341 4.6 28.7 1.0 OD1 A:ASP176 4.6 33.5 1.0 N A:ALA369 4.7 31.1 1.0 CB A:ASP367 4.7 36.1 1.0

Calcium 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 Calcium with other atoms in the Ca 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:Ca901 b:28.7 occ:1.00 O B:HOH1098 2.3 31.7 1.0 O B:HOH1267 2.4 32.4 1.0 O B:HOH1158 2.4 26.3 1.0 OD1 B:ASP176 2.5 29.9 1.0 OD1 B:ASP367 2.5 28.8 1.0 OD1 B:ASP341 2.6 25.3 1.0 OD2 B:ASP341 2.7 30.0 1.0 CG B:ASP341 3.0 32.2 1.0 OD2 B:ASP367 3.1 27.4 1.0 CG B:ASP367 3.2 32.2 1.0 CG B:ASP176 3.5 32.1 1.0 CB B:ASP176 4.2 30.4 1.0 O B:HOH1136 4.2 33.7 1.0 NZ A:LYS854 4.4 29.6 1.0 OD2 B:ASP108 4.4 32.0 1.0 O B:HOH1271 4.5 27.6 1.0 OD2 B:ASP176 4.5 30.6 1.0 N B:ASP176 4.5 31.9 1.0 CB B:ASP341 4.5 26.0 1.0 O B:HOH1085 4.6 23.2 1.0 O B:HOH1006 4.6 30.8 1.0 CB B:ALA369 4.7 25.4 1.0 CB B:ASP367 4.7 30.4 1.0 N B:ALA369 4.8 27.6 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