Magnesium in PDB 6ed2: Faecalibacterium Prausnitzii Beta-Glucuronidase

The structure of Faecalibacterium Prausnitzii Beta-Glucuronidase, PDB code: 6ed2 was solved by S.J.Pellock, 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)	28.85 / 2.30
Space group	P 64 2 2
Cell size a, b, c (Å), α, β, γ (°)	145.232, 145.232, 233.897, 90.00, 90.00, 120.00
R / Rfree (%)	17.2 / 19.9

The binding sites of Magnesium atom in the Faecalibacterium Prausnitzii Beta-Glucuronidase (pdb code 6ed2). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Faecalibacterium Prausnitzii Beta-Glucuronidase, PDB code: 6ed2:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Faecalibacterium Prausnitzii Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Faecalibacterium Prausnitzii Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg702 b:38.2 occ:1.00 O A:ASP169 2.9 29.7 0.4 O A:HOH828 3.0 33.9 1.0 NE2 A:HIS302 3.1 28.1 1.0 OD2 A:ASP169 3.2 32.7 0.4 C A:ASP169 3.3 33.0 0.4 CZ2 A:TRP560 3.4 20.5 1.0 CB A:ASP169 3.5 37.4 0.4 NE2 A:HIS336 3.6 31.2 1.0 CD2 A:PHE170 3.6 30.0 1.0 CD2 A:HIS336 3.6 27.2 1.0 CE1 A:PHE565 3.7 26.3 1.0 CZ A:PHE565 3.7 21.8 1.0 CB A:ASP169 3.7 36.8 0.6 CG A:ASP169 3.8 39.2 0.4 CA A:ASP169 3.9 34.9 0.4 CB A:PHE170 3.9 33.9 1.0 N A:PHE170 4.0 27.3 1.0 CE1 A:HIS302 4.0 26.9 1.0 C1 A:GOL701 4.0 47.0 1.0 CD2 A:HIS302 4.1 29.9 1.0 CH2 A:TRP560 4.1 23.5 1.0 CG A:PHE170 4.2 32.1 1.0 CA A:PHE170 4.4 32.7 1.0 CE2 A:TRP560 4.4 24.8 1.0 C A:ASP169 4.4 32.8 0.6 CA A:ASP169 4.4 32.8 0.6 N A:ASP169 4.4 34.1 0.4 CG A:ASP169 4.5 35.9 0.6 N A:ASP169 4.5 34.2 0.6 CE2 A:PHE170 4.6 31.6 1.0 OD1 A:ASP169 4.6 31.6 0.6 NE1 A:TRP560 4.7 26.8 1.0 CD1 A:PHE565 4.8 26.5 1.0 O1 A:GOL701 4.8 44.3 1.0 CE1 A:HIS336 4.8 25.2 1.0 CE2 A:PHE565 4.9 26.6 1.0 OD1 A:ASP169 5.0 40.7 0.4 CG A:HIS336 5.0 28.6 1.0

Magnesium binding site 2 out of 2 in the Faecalibacterium Prausnitzii Beta-Glucuronidase


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Faecalibacterium Prausnitzii Beta-Glucuronidase within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg703 b:48.4 occ:1.00 OG1 A:THR219 2.7 42.4 1.0 OE1 A:GLU221 2.8 49.5 1.0 O A:VAL258 3.0 28.9 1.0 O A:THR219 3.2 34.2 1.0 C A:THR219 3.5 32.0 1.0 CD A:GLU221 3.5 43.7 1.0 CG A:GLU221 3.5 38.4 1.0 CG A:ARG260 3.6 35.2 1.0 CB A:ARG260 3.7 33.1 1.0 N A:ARG260 3.7 28.8 1.0 C A:VAL258 3.8 28.7 1.0 CG1 A:VAL258 3.8 27.4 1.0 N A:VAL220 3.8 29.5 1.0 CB A:THR219 3.9 35.9 1.0 N A:GLU221 3.9 32.3 1.0 CD A:ARG260 3.9 36.0 1.0 CA A:VAL220 3.9 28.9 1.0 C A:VAL220 4.1 33.8 1.0 CB A:GLU221 4.1 32.7 1.0 C A:ILE259 4.2 29.7 1.0 CB A:VAL258 4.3 33.3 1.0 CA A:ILE259 4.3 28.8 1.0 CA A:THR219 4.3 28.3 1.0 CA A:ARG260 4.3 31.3 1.0 N A:ILE259 4.3 26.6 1.0 CA A:GLU221 4.7 33.6 1.0 OE2 A:GLU221 4.7 43.6 1.0 CA A:VAL258 4.7 29.1 1.0 O A:VAL220 4.8 32.0 1.0 NE A:ARG260 4.9 41.3 1.0 N A:THR219 5.0 29.2 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