Calcium in PDB 7pxq: GH115 Alpha-1,2-Glucuronidase D303A

All present enzymatic activity of GH115 Alpha-1,2-Glucuronidase D303A:
3.2.1.131;

The structure of GH115 Alpha-1,2-Glucuronidase D303A, PDB code: 7pxq 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)	50.47 / 2.30
Space group	P 61 2 2
Cell size a, b, c (Å), α, β, γ (°)	148.15, 148.15, 274.46, 90, 90, 120
R / Rfree (%)	19 / 21.9

The binding sites of Calcium atom in the GH115 Alpha-1,2-Glucuronidase D303A (pdb code 7pxq). 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 D303A, PDB code: 7pxq:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in the GH115 Alpha-1,2-Glucuronidase D303A


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 D303A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca901 b:63.0 occ:1.00 O A:LYS416 2.2 65.9 1.0 O A:HOH1091 2.2 54.9 1.0 OD2 A:ASP448 2.3 63.3 1.0 O A:HOH1130 2.3 60.2 1.0 O A:HOH1183 2.4 61.4 1.0 O A:HOH1115 2.5 60.5 1.0 C A:LYS416 3.3 62.1 1.0 CG A:ASP448 3.5 65.8 1.0 CA A:LYS416 4.1 64.4 1.0 O A:HOH1082 4.1 62.7 1.0 OD1 A:ASP448 4.1 68.1 1.0 O A:HOH1134 4.2 57.4 1.0 CB A:LYS416 4.3 62.6 1.0 OD2 A:ASP407 4.3 65.5 1.0 N A:TRP417 4.3 61.3 1.0 O A:HOH1101 4.4 54.9 1.0 O A:TRP417 4.4 63.5 1.0 O A:HOH1167 4.4 58.6 1.0 CA A:TRP417 4.5 62.6 1.0 CB A:ASP448 4.6 62.9 1.0 N A:ASP448 4.6 61.7 1.0 O A:ASP177 4.6 67.0 1.0 OD1 A:ASP407 4.6 62.8 1.0 CB A:ALA181 4.7 63.5 1.0 OE1 A:GLN625 4.7 68.6 1.0 CB A:GLN625 4.7 62.0 1.0 C A:TRP417 4.8 58.5 1.0 CG A:GLN625 4.9 63.6 1.0 CG A:ASP407 4.9 68.0 1.0

Calcium binding site 2 out of 3 in the GH115 Alpha-1,2-Glucuronidase D303A


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 D303A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca902 b:105.8 occ:1.00 O A:HOH1230 2.4 100.2 1.0 O A:HOH1043 2.4 81.3 1.0 O A:HOH1226 2.6 91.7 1.0 OD1 A:ASP439 2.6 88.4 1.0 OD2 A:ASP439 2.6 85.0 1.0 O A:HOH1271 2.7 86.9 1.0 O A:HOH1246 2.8 85.1 1.0 CG A:ASP439 3.0 80.6 1.0 OE2 A:GLU440 4.3 78.0 1.0 O A:HOH1184 4.3 79.1 1.0 O A:HOH1090 4.4 75.8 1.0 CB A:ASP439 4.5 77.0 1.0 O A:HOH1009 4.5 73.9 1.0 O A:GLY437 4.7 87.4 1.0

Calcium binding site 3 out of 3 in the GH115 Alpha-1,2-Glucuronidase D303A


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 D303A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca903 b:81.0 occ:1.00 OD2 A:ASP640 2.4 66.5 1.0 O A:HOH1260 2.5 77.3 1.0 O A:HOH1266 2.5 81.2 1.0 O A:HOH1237 2.5 75.6 1.0 O A:HOH1135 2.6 70.2 1.0 O A:HOH1214 2.6 77.0 1.0 O A:HOH1083 2.8 72.0 1.0 CG A:ASP640 3.3 63.7 1.0 CB A:ASP640 3.6 64.7 1.0 NZ A:LYS627 4.0 61.2 1.0 OD2 A:ASP603 4.3 58.3 1.0 OD1 A:ASP640 4.5 65.8 1.0 O A:HOH1251 4.5 78.2 1.0 O A:HOH1168 4.6 64.1 1.0 OG A:SER607 4.7 56.5 1.0 CB A:ALA604 4.8 56.8 1.0 O A:HOH1048 4.8 76.4 1.0 N A:ASP640 4.8 70.3 1.0 CA A:ASP640 4.8 71.9 1.0 CA A:ALA604 4.9 65.3 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