Calcium in PDB 5nmr: Monomeric Mouse Sortilin Extracellular Domain

The structure of Monomeric Mouse Sortilin Extracellular Domain, PDB code: 5nmr was solved by N.O.L.Leloup, P.Loessl, D.H.M.Meijer, A.J.R.Heck, D.M.E.Thies-Weesie, B.J.C.Janssen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	65.99 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	200.580, 62.570, 67.310, 90.00, 101.35, 90.00
R / Rfree (%)	20 / 23.3

The binding sites of Calcium atom in the Monomeric Mouse Sortilin Extracellular Domain (pdb code 5nmr). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Monomeric Mouse Sortilin Extracellular Domain, PDB code: 5nmr:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Monomeric Mouse Sortilin Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Monomeric Mouse Sortilin Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca806 b:64.7 occ:1.00 O A:THR518 2.3 32.1 1.0 O A:SER616 2.3 44.6 1.0 O A:HOH1063 2.4 37.0 1.0 O A:HOH1066 2.4 31.8 1.0 C A:SER616 3.5 43.8 1.0 O A:LYS614 3.5 39.9 1.0 C A:THR518 3.6 32.6 1.0 O A:ARG613 3.6 33.9 1.0 CD2 A:LEU612 3.8 29.7 1.0 C A:LYS614 4.2 43.7 1.0 CG A:LEU612 4.2 34.5 1.0 O A:HOH1031 4.3 45.7 1.0 O A:GLY499 4.3 30.9 1.0 N A:SER616 4.4 40.2 1.0 O A:HOH999 4.4 29.6 1.0 N A:VAL617 4.4 40.3 1.0 CA A:THR518 4.5 33.7 1.0 CA A:SER616 4.5 42.0 1.0 N A:ASP519 4.5 32.0 1.0 CA A:VAL617 4.5 41.6 1.0 CA A:ASP519 4.5 35.1 1.0 CB A:THR518 4.5 36.6 1.0 CA A:LYS614 4.6 42.5 1.0 C A:ARG613 4.7 37.4 1.0 CB A:SER616 4.8 42.9 1.0 CA A:GLY499 4.9 32.7 1.0 N A:CYS618 4.9 35.4 1.0 C A:SER615 4.9 41.3 1.0 O A:HOH1016 4.9 30.1 1.0

Calcium binding site 2 out of 2 in the Monomeric Mouse Sortilin Extracellular Domain


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Monomeric Mouse Sortilin Extracellular Domain within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca807 b:34.4 occ:1.00 O A:GLU334 2.3 33.1 1.0 O A:GLY336 2.3 35.3 1.0 O A:HOH1103 2.4 39.3 1.0 OD2 A:ASP333 2.4 29.7 1.0 O A:HOH1020 2.4 34.7 1.0 O A:HOH980 2.4 33.9 1.0 OD1 A:ASP333 2.5 28.2 1.0 CG A:ASP333 2.7 28.3 1.0 C A:GLU334 3.5 33.5 1.0 C A:GLY336 3.5 37.1 1.0 N A:GLY336 4.0 40.9 1.0 C A:PRO335 4.1 42.8 1.0 N A:GLU334 4.1 31.2 1.0 CB A:ASP333 4.3 24.8 1.0 CA A:GLY336 4.4 42.1 1.0 CA A:GLU334 4.4 34.2 1.0 O A:PRO335 4.4 45.6 1.0 CA A:PRO335 4.5 37.6 1.0 N A:PRO335 4.5 32.4 1.0 N A:ASP337 4.5 35.3 1.0 O A:PHE340 4.5 26.4 1.0 N A:THR338 4.5 44.6 1.0 C A:ASP333 4.6 27.1 1.0 CA A:ASP337 4.6 42.0 1.0 O A:GLU315 4.7 36.1 1.0 OG1 A:THR338 4.7 37.6 1.0 CG A:GLN316 4.7 31.6 1.0 O A:HOH1049 4.9 45.1 1.0 N A:GLY339 4.9 30.9 1.0 CA A:ASP333 4.9 24.4 1.0

N.Leloup, P.Lossl, D.H.Meijer, M.Brennich, A.J.R.Heck, D.M.E.Thies-Weesie, B.J.C.Janssen. Low pH-Induced Conformational Change and Dimerization of Sortilin Triggers Endocytosed Ligand Release. Nat Commun V. 8 1708 2017.
ISSN: ESSN 2041-1723
PubMed: 29167428
DOI: 10.1038/S41467-017-01485-5