Calcium in PDB 7pug: GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose

All present enzymatic activity of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose:
3.2.1.131;

The structure of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose, PDB code: 7pug was solved by C.Wilkens, J.P.Morth, I.Polikarpov, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.26 / 2.66
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	148.63, 148.63, 272.79, 90, 90, 120
R / Rfree (%)	17.4 / 21

The structure of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose also contains other interesting chemical elements:

Chlorine

(Cl)

13 atoms

The binding sites of Calcium atom in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose (pdb code 7pug). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 3 binding sites of Calcium where determined in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose, PDB code: 7pug:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca914 b:74.0 occ:1.00 OD2 A:ASP448 2.2 76.9 1.0 O A:HOH1031 2.3 61.4 1.0 O A:LYS416 2.3 81.9 1.0 O A:HOH1124 2.3 70.3 1.0 O A:HOH1184 2.5 74.3 1.0 O A:HOH1094 2.5 71.2 1.0 C A:LYS416 3.4 73.2 1.0 CG A:ASP448 3.4 79.5 1.0 O A:HOH1091 3.8 77.3 1.0 O A:HOH1074 4.1 76.0 1.0 CA A:LYS416 4.1 73.7 1.0 OD1 A:ASP448 4.1 79.1 1.0 CB A:LYS416 4.2 71.0 1.0 OD1 A:ASP407 4.2 74.5 1.0 O A:HOH1076 4.3 69.7 1.0 O A:HOH1168 4.4 75.3 1.0 N A:TRP417 4.4 78.7 1.0 CB A:ASP448 4.5 69.8 1.0 N A:ASP448 4.6 75.4 1.0 O A:TRP417 4.6 73.0 1.0 CB A:ALA181 4.6 81.4 1.0 CA A:TRP417 4.6 72.2 1.0 O A:ASP177 4.6 85.9 1.0 CB A:GLN625 4.7 73.4 1.0 OE1 A:GLN625 4.7 84.2 1.0 OD2 A:ASP407 4.9 80.7 1.0 CG A:GLN625 4.9 74.8 1.0 C A:TRP417 4.9 68.7 1.0 CG A:ASP407 4.9 80.0 1.0

Calcium binding site 2 out of 3 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca915 b:150.0 occ:1.00 O A:HOH1146 3.2 93.3 1.0 O A:HOH1275 3.4 106.1 1.0 O A:HOH1048 3.4 90.1 1.0 O A:HOH1013 3.5 82.3 1.0 O A:HOH1298 3.7 99.1 1.0 OE1 A:GLU440 3.8 108.8 1.0 OD1 A:ASP439 4.1 98.0 1.0 O A:HOH1064 4.7 83.9 1.0 CG A:ASP439 4.8 94.6 1.0 OD2 A:ASP439 4.9 103.8 1.0 CD A:GLU440 5.0 112.0 1.0

Calcium binding site 3 out of 3 in the GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of GH115 Alpha-1,2-Glucuronidase in Complex with Xylopentaose within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca916 b:98.1 occ:1.00 OD2 A:ASP640 2.6 88.3 1.0 O A:HOH1026 2.6 84.3 1.0 O A:HOH1226 2.7 89.5 1.0 O A:HOH1287 2.7 94.3 1.0 O A:HOH1196 3.1 88.9 1.0 O A:HOH1221 3.4 84.6 1.0 CG A:ASP640 3.6 83.5 1.0 CB A:ASP640 3.8 80.3 1.0 NZ A:LYS627 4.3 78.4 1.0 O A:HOH1254 4.4 92.2 1.0 CB A:ALA604 4.4 65.2 1.0 OD2 A:ASP603 4.5 78.4 1.0 OD1 A:ASP640 4.7 81.6 1.0 CA A:ALA604 4.7 65.5 1.0 OG A:SER607 4.7 72.5 1.0 N A:ASP640 5.0 82.2 1.0

C.Wilkens, M.Vuillemin, B.Pilgaard, I.Polikarpov, J.P.Morth. A GH115 Alpha-Glucuronidase Structure Reveals Dimerization-Mediated Substrate Binding and A Proton Wire Potentially Important For Catalysis. Acta Crystallogr D Struct V. 78 658 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35503213
DOI: 10.1107/S2059798322003527