Calcium in PDB 1ups: Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens

The structure of Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens, PDB code: 1ups was solved by W.Tempel, Z.-J.Liu, P.S.Horanyi, L.Deng, D.Lee, M.G.Newton, J.P.Rose, H.Ashida, S.-C.Li, Y.-T.Li, B.-C.Wang, Southeast Collaboratory Forstructural Genomics (Secsg), with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.82
Space group	P 63
Cell size a, b, c (Å), α, β, γ (°)	160.430, 160.430, 86.140, 90.00, 90.00, 120.00
R / Rfree (%)	17.6 / 20.4

The binding sites of Calcium atom in the Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens (pdb code 1ups). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens, PDB code: 1ups:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca501 b:18.8 occ:1.00 O A:GLU37 2.3 14.7 1.0 O A:GLY72 2.4 15.1 1.0 O A:ASP272 2.4 10.2 1.0 OD2 A:ASP272 2.4 13.3 1.0 O A:HOH2015 2.4 19.9 1.0 O A:HOH2126 2.5 22.0 1.0 OD1 A:ASN39 2.9 18.5 0.7 C A:ASP272 3.4 11.2 1.0 C A:GLU37 3.5 14.2 1.0 CG A:ASP272 3.5 13.5 1.0 C A:GLY72 3.5 15.3 1.0 CA A:ASP272 3.9 11.0 1.0 CG A:ASN39 4.1 19.2 0.7 CA A:GLY72 4.1 16.7 1.0 CA A:GLU37 4.2 14.3 1.0 O A:HOH2127 4.3 30.8 1.0 CB A:ASP272 4.3 10.9 1.0 O A:PHE38 4.4 17.4 1.0 OD1 A:ASP272 4.4 10.8 1.0 CB A:GLU37 4.4 13.6 1.0 C A:PHE38 4.4 16.5 1.0 O A:HOH2031 4.5 27.6 1.0 N A:TYR273 4.5 10.8 1.0 N A:PHE38 4.5 15.0 1.0 N A:SER73 4.6 13.9 1.0 ND2 A:ASN39 4.7 16.9 0.7 OE2 A:GLU37 4.7 16.7 1.0 N A:ASN39 4.7 17.8 1.0 CB A:TYR273 4.8 11.1 1.0 CB A:PHE38 4.8 14.8 1.0 CA A:PHE38 4.8 15.2 1.0 CA A:TYR273 4.9 10.9 1.0 CA A:SER73 4.9 13.4 1.0

Calcium binding site 2 out of 2 in the Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Glcnac[Alpha]1-4GAL Releasing Endo-[Beta]-Galactosidase From Clostridium Perfringens within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca501 b:21.4 occ:1.00 OD2 B:ASP272 2.3 15.6 1.0 O B:GLY72 2.3 15.7 1.0 O B:HOH2012 2.3 25.2 1.0 O B:GLU37 2.4 14.7 1.0 O B:ASP272 2.4 10.8 1.0 O B:HOH2130 2.4 23.0 1.0 OD1 B:ASN39 2.7 23.3 1.0 CG B:ASP272 3.4 13.6 1.0 C B:ASP272 3.4 12.2 1.0 C B:GLY72 3.5 16.4 1.0 C B:GLU37 3.5 14.9 1.0 CG B:ASN39 3.8 23.7 1.0 CA B:ASP272 3.9 12.2 1.0 CA B:GLY72 4.0 17.8 1.0 CA B:GLU37 4.2 14.7 1.0 OD1 B:ASP272 4.2 14.3 1.0 O B:HOH2028 4.2 32.9 1.0 CB B:ASP272 4.3 12.0 1.0 CB B:GLU37 4.4 14.8 1.0 ND2 B:ASN39 4.4 24.1 1.0 C B:PHE38 4.4 18.1 1.0 O B:PHE38 4.5 18.8 1.0 N B:TYR273 4.5 12.2 1.0 N B:PHE38 4.6 15.7 1.0 N B:SER73 4.6 15.4 1.0 N B:ASN39 4.7 19.5 1.0 OE2 B:GLU37 4.7 15.9 1.0 CB B:TYR273 4.8 13.1 1.0 CB B:PHE38 4.8 16.4 1.0 CA B:PHE38 4.8 16.3 1.0 CA B:ASN39 4.9 21.1 1.0 CA B:TYR273 4.9 12.6 1.0 CA B:SER73 4.9 15.0 1.0 CB B:ASN39 5.0 21.6 1.0

W.Tempel, Z.J.Liu, P.S.Horanyi, L.Deng, D.Lee, M.G.Newton, J.P.Rose, H.Ashida, S.C.Li, Y.T.Li, B.C.Wang. Three-Dimensional Structure of GLCNACALPHA1-4GAL Releasing Endo-Beta-Galactosidase From Clostridium Perfringens. Proteins V. 59 141 2005.
ISSN: ESSN 1097-0134
PubMed: 15688452
DOI: 10.1002/PROT.20363