Calcium in PDB 5b4y: Crystal Structure of the LA12 Fragment of APOER2

The structure of Crystal Structure of the LA12 Fragment of APOER2, PDB code: 5b4y was solved by T.Nogi, S.Tabata, H.Hirai, N.Yasui, J.Takagi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.28 / 1.90
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	31.162, 41.780, 55.063, 90.00, 90.00, 90.00
R / Rfree (%)	21 / 24.7

The binding sites of Calcium atom in the Crystal Structure of the LA12 Fragment of APOER2 (pdb code 5b4y). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Crystal Structure of the LA12 Fragment of APOER2, PDB code: 5b4y:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Crystal Structure of the LA12 Fragment of APOER2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Crystal Structure of the LA12 Fragment of APOER2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3001 b:23.8 occ:1.00 O B:ASP68 2.2 30.5 1.0 OD2 B:ASP66 2.2 24.6 1.0 OD2 B:ASP70 2.2 24.5 1.0 O B:TRP63 2.3 22.0 1.0 OD2 B:ASP76 2.3 23.9 1.0 OE2 B:GLU77 2.3 28.5 1.0 CG B:ASP66 3.2 24.6 1.0 CG B:ASP70 3.3 25.8 1.0 C B:ASP68 3.4 29.7 1.0 CD B:GLU77 3.4 26.7 1.0 CG B:ASP76 3.5 22.7 1.0 C B:TRP63 3.5 23.4 1.0 OD1 B:ASP66 3.8 24.0 1.0 CG B:GLU77 4.0 26.3 1.0 N B:ASP68 4.0 30.1 1.0 N B:ASP70 4.0 27.4 1.0 CB B:ASP70 4.0 25.9 1.0 N B:ASP66 4.1 28.0 1.0 CA B:ASP68 4.1 29.9 0.4 CB B:ASP76 4.1 22.3 1.0 OD1 B:ASP70 4.1 29.8 1.0 CB B:ASP68 4.1 29.1 0.4 CA B:ASP68 4.2 31.4 0.6 CB B:TRP63 4.2 23.8 1.0 CA B:TRP63 4.2 22.5 1.0 CB B:ASP66 4.3 24.8 1.0 OD1 B:ASP76 4.4 24.3 1.0 N B:ASP69 4.4 28.9 1.0 OE1 B:GLU77 4.5 27.2 1.0 CB B:ASP68 4.5 33.5 0.6 N B:CYS65 4.5 28.2 1.0 N B:ARG64 4.5 24.6 1.0 N B:GLU67 4.6 30.1 1.0 CA B:ASP66 4.6 26.6 1.0 CA B:ASP69 4.6 31.6 1.0 O B:ASP76 4.7 24.7 1.0 C B:ASP66 4.7 29.1 1.0 CA B:ASP70 4.7 27.2 1.0 CA B:ARG64 4.7 27.9 1.0 C B:ASP69 4.8 29.2 1.0 C B:ARG64 4.8 26.7 1.0 C B:ASP76 4.9 23.0 1.0 CD1 B:ILE59 4.9 20.8 1.0

Calcium binding site 2 out of 2 in the Crystal Structure of the LA12 Fragment of APOER2


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Crystal Structure of the LA12 Fragment of APOER2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca3002 b:37.6 occ:1.00 O B:GLU107 2.0 39.3 1.0 OE2 B:GLU116 2.1 34.3 1.0 O B:TRP102 2.3 47.1 1.0 OE1 B:GLU109 2.3 43.6 1.0 OD2 B:ASP115 2.4 29.0 1.0 OD2 B:ASP105 2.7 50.5 1.0 CD B:GLU116 3.2 36.2 1.0 C B:GLU107 3.3 38.4 1.0 CD B:GLU109 3.4 38.9 1.0 C B:TRP102 3.5 50.9 1.0 CG B:ASP115 3.5 31.3 1.0 CG B:ASP105 3.6 51.5 1.0 CG B:GLU116 3.8 34.1 1.0 N B:GLU107 3.9 38.0 1.0 N B:GLU109 3.9 31.1 1.0 N B:ASP105 4.0 57.1 1.0 OE2 B:GLU109 4.0 41.9 1.0 CA B:GLU107 4.1 38.3 1.0 OD1 B:ASP105 4.1 58.2 1.0 CB B:TRP102 4.2 50.3 1.0 N B:CYS104 4.2 48.4 1.0 OE1 B:GLU116 4.2 40.9 1.0 N B:GLU108 4.3 33.3 1.0 CB B:ASP115 4.3 29.8 1.0 CA B:TRP102 4.3 49.9 1.0 OD1 B:ASP115 4.4 30.1 1.0 CA B:GLU108 4.4 32.3 1.0 CB B:GLU109 4.5 35.6 1.0 N B:LYS103 4.5 52.0 1.0 CB B:GLU107 4.5 38.7 1.0 N B:GLY106 4.5 47.0 1.0 CG B:GLU109 4.6 36.7 1.0 C B:LYS103 4.6 50.5 1.0 C B:ASP105 4.6 48.9 1.0 CA B:ASP105 4.6 50.3 1.0 O B:HOH3106 4.6 42.0 1.0 O B:ASP115 4.6 32.8 1.0 CA B:LYS103 4.6 52.7 1.0 C B:GLU108 4.7 29.1 1.0 CB B:ASP105 4.7 50.6 1.0 CA B:GLU109 4.8 32.4 1.0 C B:GLY106 4.9 39.7 1.0 C B:ASP115 4.9 31.6 1.0 C B:CYS104 4.9 59.6 1.0 CA B:CYS104 4.9 54.4 1.0

H.Hirai, N.Yasui, K.Yamashita, S.Tabata, M.Yamamoto, J.Takagi, T.Nogi. Crystal Structure of the Ectodomain From A Ldlr Close Homologue in Complex with Its Physiological Ligand. To Be Published.