Calcium in PDB 6mvg: Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus

The structure of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus, PDB code: 6mvg was solved by 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)	29.88 / 2.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	236.028, 127.078, 88.819, 90.00, 98.49, 90.00
R / Rfree (%)	18.5 / 24.6

The binding sites of Calcium atom in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus (pdb code 6mvg). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus, PDB code: 6mvg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus


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 Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca802 b:65.2 occ:1.00 O A:GLY45 2.2 55.7 1.0 OD1 A:ASP44 2.2 52.8 1.0 OD1 A:ASP48 2.3 55.4 1.0 OD1 A:ASP521 2.4 53.8 1.0 O A:ASP41 2.5 47.3 1.0 OD2 A:ASP521 2.8 54.0 1.0 CG A:ASP521 3.0 55.0 1.0 N A:GLY45 3.0 54.3 1.0 C A:GLY45 3.2 56.7 1.0 CG A:ASP48 3.2 56.0 1.0 CG A:ASP44 3.4 56.6 1.0 C A:ASP41 3.4 47.6 1.0 OD2 A:ASP48 3.5 57.2 1.0 CA A:GLY45 3.6 58.5 1.0 C A:ASP44 3.7 53.2 1.0 N A:ASP44 3.8 51.4 1.0 CA A:ASP41 3.9 42.4 1.0 CA A:ASP44 4.1 48.1 1.0 OD2 A:ASP44 4.2 55.8 1.0 N A:ASP48 4.3 58.0 1.0 CB A:ASP44 4.3 54.8 1.0 N A:GLY42 4.4 50.2 1.0 N A:TYR49 4.4 46.2 1.0 N A:GLY46 4.4 57.8 1.0 CB A:ASP521 4.5 50.7 1.0 CB A:ASP41 4.5 49.5 1.0 N A:GLN43 4.5 42.6 1.0 O A:ASP44 4.5 54.5 1.0 CB A:ASP48 4.6 49.8 1.0 C A:GLY42 4.6 42.6 1.0 CA A:GLY42 4.6 43.3 1.0 N A:ASN47 4.7 54.4 1.0 NZ C:LYS10 4.7 49.9 1.0 CA A:ASP48 4.8 50.4 1.0 C A:ASP48 4.8 52.3 1.0 CB A:TYR49 4.9 45.7 1.0 C A:GLN43 4.9 51.9 1.0 O A:ASP521 4.9 53.3 1.0 C A:GLY46 4.9 51.9 1.0 CA A:GLY46 4.9 53.3 1.0 CA A:TYR49 4.9 48.2 1.0

Calcium binding site 2 out of 3 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus


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 Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca802 b:63.2 occ:1.00 O B:ASP41 2.2 47.4 1.0 OD1 B:ASP48 2.2 55.7 1.0 OD1 B:ASP44 2.2 54.2 1.0 OD1 B:ASP521 2.2 50.5 1.0 OD2 B:ASP521 2.5 55.9 1.0 O B:GLY45 2.5 54.3 1.0 CG B:ASP521 2.7 51.4 1.0 CG B:ASP48 3.3 59.8 1.0 C B:ASP41 3.3 44.4 1.0 CG B:ASP44 3.4 48.2 1.0 N B:GLY45 3.5 47.8 1.0 C B:GLY45 3.6 55.6 1.0 N B:ASP48 3.8 55.9 1.0 OD2 B:ASP48 3.9 66.2 1.0 N B:TYR49 4.0 48.3 1.0 OD2 B:ASP44 4.1 49.3 1.0 CA B:GLY45 4.1 48.5 1.0 C B:ASP44 4.1 48.3 1.0 CA B:ASP41 4.1 44.1 1.0 CB B:ASP521 4.1 50.2 1.0 N B:ASP44 4.2 49.6 1.0 N B:GLY42 4.3 43.0 1.0 C B:ASP48 4.3 49.7 1.0 CA B:GLY42 4.4 48.3 1.0 CA B:ASP48 4.4 47.9 1.0 CB B:ASP48 4.4 49.0 1.0 N B:ASN47 4.4 56.3 1.0 CA B:ASP44 4.5 45.0 1.0 CB B:ASP41 4.5 44.2 1.0 CB B:TYR49 4.5 42.7 1.0 CB B:ASP44 4.5 42.8 1.0 CA B:TYR49 4.6 49.0 1.0 O B:ASP521 4.7 53.6 1.0 N B:GLY46 4.7 63.5 1.0 C B:GLY42 4.7 47.6 1.0 N B:GLN43 4.8 41.4 1.0 C B:ASN47 4.9 59.6 1.0 C B:GLY46 4.9 61.3 1.0 CA B:ASP521 4.9 51.2 1.0 O B:ASP44 4.9 50.5 1.0 CA B:ASN47 5.0 53.9 1.0

Calcium binding site 3 out of 3 in the Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Crystal Structure of Fmn-Binding Beta-Glucuronidase From Ruminococcus Gnavus within 5.0Å range: probe atom residue distance (Å) B Occ C:Ca802 b:70.4 occ:1.00 OD1 C:ASP48 2.0 52.1 1.0 OD1 C:ASP44 2.3 54.6 1.0 OD2 C:ASP521 2.3 54.6 1.0 O C:ASP41 2.4 57.4 1.0 O C:GLY45 2.4 62.8 1.0 OD1 C:ASP521 2.4 54.8 1.0 CG C:ASP521 2.7 54.8 1.0 CG C:ASP48 3.1 55.0 1.0 C C:GLY45 3.3 57.1 1.0 C C:ASP41 3.4 53.1 1.0 CG C:ASP44 3.4 58.0 1.0 OD2 C:ASP48 3.5 59.0 1.0 N C:GLY45 3.7 58.8 1.0 C C:ASP44 3.9 58.8 1.0 CA C:ASP41 4.0 48.5 1.0 CA C:GLY45 4.0 59.5 1.0 OD2 C:ASP44 4.0 57.9 1.0 N C:ASP48 4.0 52.5 1.0 N C:TYR49 4.1 49.8 1.0 N C:ASP44 4.2 55.9 1.0 O C:ASP44 4.2 59.8 1.0 N C:GLY46 4.2 51.8 1.0 CB C:ASP521 4.2 52.7 1.0 CB C:ASP48 4.3 53.7 1.0 CB C:ASP41 4.4 49.4 1.0 CA C:ASP44 4.4 55.8 1.0 C C:ASP48 4.4 53.9 1.0 N C:GLY42 4.5 50.7 1.0 CA C:ASP48 4.5 53.1 1.0 CB C:ASP44 4.5 58.6 1.0 CA C:GLY46 4.6 44.5 1.0 CA C:GLY42 4.6 51.2 1.0 CA C:TYR49 4.7 49.7 1.0 CB C:TYR49 4.7 48.2 1.0 N C:ASN47 4.8 55.1 1.0 N C:GLN43 4.8 54.1 1.0 O C:ASP521 4.8 54.4 1.0 C C:GLY46 4.9 51.9 1.0 C C:GLY42 4.9 52.6 1.0 NZ A:LYS10 4.9 53.5 1.0

S.J.Pellock, W.G.Walton, S.M.Ervin, D.Torres-Rivera, B.C.Creekmore, G.Bergan, Z.D.Dunn, B.Li, A.Tripathy, M.R.Redinbo. Discovery and Characterization of Fmn-Binding Beta-Glucuronidases in the Human Gut Microbiome. J. Mol. Biol. V. 431 970 2019.
ISSN: ESSN 1089-8638
PubMed: 30658055
DOI: 10.1016/J.JMB.2019.01.013