Calcium in PDB 5nxb: Mouse Galactocerebrosidase in Complex with Saposin A

All present enzymatic activity of Mouse Galactocerebrosidase in Complex with Saposin A:
3.2.1.46;

The structure of Mouse Galactocerebrosidase in Complex with Saposin A, PDB code: 5nxb was solved by S.C.Graham, C.H.Hill, J.E.Deane, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	162.11 / 3.60
Space group	P 62 2 2
Cell size a, b, c (Å), α, β, γ (°)	187.183, 187.183, 360.240, 90.00, 90.00, 120.00
R / Rfree (%)	21.7 / 23.1

The binding sites of Calcium atom in the Mouse Galactocerebrosidase in Complex with Saposin A (pdb code 5nxb). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Mouse Galactocerebrosidase in Complex with Saposin A, PDB code: 5nxb:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Mouse Galactocerebrosidase in Complex with Saposin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Mouse Galactocerebrosidase in Complex with Saposin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca709 b:0.5 occ:1.00 O A:ASP477 2.3 0.7 1.0 OD1 A:ASP660 2.3 0.3 1.0 OD1 A:ASN479 2.4 0.9 1.0 O A:PHE511 2.4 0.2 1.0 CG A:ASP660 3.0 0.5 1.0 OD2 A:ASP660 3.0 0.9 1.0 CG A:ASN479 3.3 1.0 1.0 C A:ASP477 3.6 0.4 1.0 C A:PHE511 3.6 0.9 1.0 ND2 A:ASN479 3.7 0.1 1.0 OD1 A:ASN661 4.2 0.8 1.0 CA A:PHE511 4.3 0.3 1.0 CB A:PHE511 4.3 0.9 1.0 N A:ASN479 4.3 0.3 1.0 CA A:ASP477 4.4 0.0 1.0 N A:PHE511 4.4 0.7 1.0 C A:PHE478 4.4 0.3 1.0 CB A:ASP477 4.4 0.2 1.0 CB A:ASP660 4.5 0.2 1.0 CB A:ASN479 4.5 0.0 1.0 N A:PHE478 4.6 0.6 1.0 N A:THR512 4.6 0.2 1.0 CA A:ASN479 4.6 0.5 1.0 CB A:PHE478 4.7 0.9 1.0 CA A:PHE478 4.8 0.1 1.0 O A:PHE478 4.8 0.7 1.0 N A:ASN661 4.8 0.2 1.0 CA A:THR512 4.8 0.0 1.0 CG A:ASN661 4.9 0.9 1.0

Calcium binding site 2 out of 2 in the Mouse Galactocerebrosidase in Complex with Saposin A


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Mouse Galactocerebrosidase in Complex with Saposin A within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca709 b:0.9 occ:1.00 OD1 B:ASP660 2.4 0.6 1.0 OD1 B:ASN479 2.6 0.9 1.0 OD2 B:ASP660 2.7 0.9 1.0 O B:PHE511 2.8 0.1 1.0 O B:ASP477 2.9 0.8 1.0 CG B:ASP660 2.9 0.7 1.0 CG B:ASN479 3.4 0.2 1.0 ND2 B:ASN479 3.6 0.8 1.0 OD1 B:ASN661 3.7 0.4 1.0 C B:PHE511 4.0 0.6 1.0 C B:ASP477 4.1 0.3 1.0 CB B:ASP660 4.4 0.7 1.0 CG B:ASN661 4.4 0.1 1.0 N B:PHE511 4.5 0.1 1.0 ND2 B:ASN661 4.6 0.8 1.0 CB B:ASP477 4.6 0.3 1.0 CA B:PHE511 4.6 0.0 1.0 CA B:ASP477 4.7 0.1 1.0 CB B:PHE511 4.7 0.0 1.0 CB B:ASN479 4.8 0.9 1.0 N B:ASN661 4.8 0.9 1.0 N B:ASN479 4.9 1.0 1.0

C.H.Hill, G.M.Cook, S.J.Spratley, S.Fawke, S.C.Graham, J.E.Deane. The Mechanism of Glycosphingolipid Degradation Revealed By A Galc-Sapa Complex Structure. Nat Commun V. 9 151 2018.
ISSN: ESSN 2041-1723
PubMed: 29323104
DOI: 10.1038/S41467-017-02361-Y