Calcium in PDB 6nzg: Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine

All present enzymatic activity of Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine:
3.2.1.23; 3.2.1.31;

The structure of Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine, PDB code: 6nzg was solved by S.J.Pellock, P.B.Jariwala, M.R.Redinbo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.46 / 2.43
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	74.536, 142.407, 180.664, 90.00, 90.00, 90.00
R / Rfree (%)	17 / 22.1

The structure of Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine also contains other interesting chemical elements:

Potassium

(K)

2 atoms

The binding sites of Calcium atom in the Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine (pdb code 6nzg). 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 Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine, PDB code: 6nzg:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca904 b:35.0 occ:1.00 O A:HOH1030 2.3 28.2 1.0 OD2 A:ASP176 2.4 33.7 1.0 O A:HOH1122 2.4 26.3 1.0 OD1 A:ASP367 2.5 32.7 1.0 O A:HOH1225 2.6 30.6 1.0 OD2 A:ASP341 2.6 33.8 1.0 OD1 A:ASP341 2.7 31.0 1.0 CG A:ASP341 3.0 34.9 1.0 OD2 A:ASP367 3.2 36.6 1.0 CG A:ASP367 3.2 34.5 1.0 CG A:ASP176 3.4 33.0 1.0 CB A:ASP176 4.1 31.8 1.0 O A:HOH1095 4.2 36.6 1.0 OD2 A:ASP108 4.3 33.8 1.0 OD1 A:ASP176 4.3 26.7 1.0 NZ B:LYS854 4.4 30.6 1.0 O A:HOH1088 4.5 29.7 1.0 N A:ASP176 4.5 30.6 1.0 CB A:ASP341 4.5 27.2 1.0 O A:HOH1057 4.6 28.6 1.0 CB A:ASP367 4.7 27.0 1.0 CB A:ALA369 4.8 27.6 1.0 CA A:ASP176 4.9 31.5 1.0 N A:ALA369 5.0 23.9 1.0

Calcium binding site 2 out of 2 in the Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Bacteroides Uniformis Beta-Glucuronidase 2 Covalently Bound to Cyclophellitol-6-Carboxylate Aziridine within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca906 b:41.8 occ:1.00 OD2 B:ASP176 2.2 35.5 1.0 O B:HOH1181 2.4 43.5 1.0 OD1 B:ASP367 2.4 47.2 1.0 O B:HOH1065 2.4 32.8 1.0 OD1 B:ASP341 2.7 42.8 1.0 O B:HOH1098 2.8 37.0 1.0 OD2 B:ASP341 2.9 40.2 1.0 OD2 B:ASP367 3.1 42.0 1.0 CG B:ASP367 3.1 39.6 1.0 CG B:ASP341 3.2 42.6 1.0 CG B:ASP176 3.4 39.0 1.0 CB B:ASP176 4.2 37.8 1.0 O B:HOH1076 4.2 41.9 1.0 O B:HOH1034 4.3 38.9 1.0 NZ A:LYS854 4.3 40.1 1.0 OD1 B:ASP176 4.4 33.6 1.0 CB B:ALA369 4.5 38.7 1.0 OD2 B:ASP108 4.5 45.0 1.0 N B:ASP176 4.6 38.7 1.0 CB B:ASP367 4.6 37.4 1.0 N B:ALA369 4.7 38.5 1.0 CB B:ASP341 4.7 37.7 1.0

P.B.Jariwala, S.J.Pellock, D.Goldfarb, E.W.Cloer, M.Artola, J.B.Simpson, A.P.Bhatt, W.G.Walton, L.R.Roberts, M.B.Major, G.J.Davies, H.S.Overkleeft, M.R.Redinbo. Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling. Acs Chem.Biol. 2019.
ISSN: ESSN 1554-8937
PubMed: 31774274
DOI: 10.1021/ACSCHEMBIO.9B00788