Calcium 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:

Sodium

(Na)

2 atoms

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

Calcium 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 Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:17.7 occ:1.00 OD2 A:ASP176 2.3 17.7 1.0 O A:HOH1087 2.4 19.1 1.0 O A:HOH1133 2.4 15.2 1.0 O A:HOH1576 2.4 19.4 1.0 OD1 A:ASP367 2.5 20.5 1.0 OD1 A:ASP341 2.5 18.3 1.0 OD2 A:ASP341 2.6 21.4 1.0 CG A:ASP341 2.9 22.2 1.0 OD2 A:ASP367 3.1 23.0 1.0 CG A:ASP367 3.1 17.3 1.0 CG A:ASP176 3.4 18.7 1.0 HZ1 B:LYS854 3.6 22.0 1.0 HB2 A:ASP176 3.7 20.8 1.0 H A:ASP176 3.7 21.8 1.0 HB2 A:ALA369 3.9 21.6 1.0 O A:HOH1037 4.1 27.3 1.0 H A:ALA369 4.1 21.3 1.0 CB A:ASP176 4.2 17.3 1.0 NZ B:LYS854 4.3 18.3 1.0 HD2 A:HIS344 4.3 22.7 1.0 OD1 A:ASP176 4.4 19.1 1.0 HZ2 B:LYS854 4.4 22.0 1.0 HZ3 B:LYS854 4.4 22.0 1.0 CB A:ASP341 4.4 15.5 1.0 HB3 A:ARG175 4.4 21.6 1.0 HZ2 A:TRP178 4.5 32.3 1.0 OD2 A:ASP108 4.5 21.6 1.0 HB3 A:ALA369 4.5 21.6 1.0 N A:ASP176 4.6 18.1 1.0 HB2 A:ASP368 4.6 22.1 1.0 O A:HOH1132 4.6 21.5 1.0 CB A:ASP367 4.6 17.9 1.0 CB A:ALA369 4.7 18.0 1.0 O A:HOH1338 4.7 18.9 1.0 H A:ASP368 4.8 24.4 1.0 HB3 A:ASP341 4.8 18.6 1.0 HE2 A:HIS344 4.8 20.7 1.0 HB2 A:ASP341 4.8 18.6 1.0 HA A:ASP341 4.9 20.7 1.0 HD3 A:ARG175 4.9 24.9 1.0 N A:ALA369 4.9 17.7 1.0 HB3 A:ASP176 4.9 20.8 1.0 HB3 A:ASP367 4.9 21.4 1.0 CD2 A:HIS344 5.0 18.9 1.0 HG2 A:ARG175 5.0 21.5 1.0 O A:HOH1082 5.0 23.1 1.0

Calcium 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 Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of Bacteroides Uniformis Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca904 b:17.2 occ:1.00 O B:HOH1148 2.4 17.4 1.0 O B:HOH1673 2.4 18.2 1.0 OD2 B:ASP176 2.4 16.6 1.0 OD1 B:ASP367 2.4 20.1 1.0 O B:HOH1227 2.5 14.3 1.0 OD1 B:ASP341 2.5 17.1 1.0 OD2 B:ASP341 2.6 20.9 1.0 CG B:ASP341 2.9 20.9 1.0 OD2 B:ASP367 3.1 21.3 1.0 CG B:ASP367 3.1 17.5 1.0 CG B:ASP176 3.5 18.6 1.0 HZ1 A:LYS854 3.5 24.2 1.0 H B:ASP176 3.7 18.8 1.0 HB2 B:ASP176 3.8 21.0 1.0 HB2 B:ALA369 3.9 17.8 1.0 H B:ALA369 4.0 20.6 1.0 O B:HOH1193 4.0 27.7 1.0 CB B:ASP176 4.2 17.5 1.0 NZ A:LYS854 4.2 20.2 1.0 HZ2 A:LYS854 4.3 24.2 1.0 HD2 B:HIS344 4.3 22.1 1.0 HZ3 A:LYS854 4.3 24.2 1.0 CB B:ASP341 4.4 16.3 1.0 HB3 B:ARG175 4.4 18.7 1.0 OD1 B:ASP176 4.4 17.2 1.0 OD2 B:ASP108 4.5 17.4 1.0 HB2 B:ASP368 4.5 21.9 1.0 O B:HOH1111 4.5 21.0 1.0 N B:ASP176 4.6 15.7 1.0 HZ2 B:TRP178 4.6 21.9 1.0 O B:HOH1272 4.6 18.5 1.0 HB3 B:ALA369 4.6 17.8 1.0 CB B:ASP367 4.6 16.7 1.0 CB B:ALA369 4.7 14.8 1.0 H B:ASP368 4.7 19.8 1.0 HB3 B:ASP341 4.7 19.5 1.0 HD3 B:ARG175 4.7 20.1 1.0 N B:ALA369 4.8 17.2 1.0 HB2 B:ASP341 4.8 19.5 1.0 HB3 B:ASP367 4.9 20.1 1.0 HA B:ASP341 4.9 22.1 1.0 O B:HOH1791 4.9 37.4 1.0 HB3 B:ASP176 5.0 21.0 1.0 HE2 B:HIS344 5.0 23.5 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