Calcium in PDB 5n4l: Rat Ceruloplasmin Trigonal Form

The structure of Rat Ceruloplasmin Trigonal Form, PDB code: 5n4l was solved by V.R.Samygina, A.V.Sokolov, G.Bourenkov, V.B.Vasilyev, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	14.99 / 3.20
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	128.230, 128.230, 407.660, 90.00, 90.00, 120.00
R / Rfree (%)	19.3 / 26.5

The structure of Rat Ceruloplasmin Trigonal Form also contains other interesting chemical elements:

Copper	(Cu)	11 atoms
Sodium	(Na)	2 atoms

The binding sites of Calcium atom in the Rat Ceruloplasmin Trigonal Form (pdb code 5n4l). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 2 binding sites of Calcium where determined in the Rat Ceruloplasmin Trigonal Form, PDB code: 5n4l:
Jump to Calcium binding site number: 1; 2;

Calcium binding site 1 out of 2 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Rat Ceruloplasmin Trigonal Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca1106 b:0.7 occ:1.00 OD1 A:ASP128 2.3 0.5 1.0 O A:LYS109 2.3 0.6 1.0 OD2 A:ASP127 2.6 0.4 1.0 OD2 A:ASP128 2.6 0.9 1.0 CG A:ASP128 2.8 0.9 1.0 O A:GLN124 3.1 0.3 1.0 OD1 A:ASP127 3.1 0.4 1.0 CG A:ASP127 3.2 0.5 1.0 OD2 A:ASP118 3.5 0.3 1.0 C A:LYS109 3.5 0.5 1.0 OE1 A:GLU112 3.7 0.2 1.0 O A:ALA114 3.7 0.1 1.0 CB A:GLU112 4.1 0.6 1.0 CE A:LYS109 4.2 0.3 1.0 C A:GLN124 4.3 0.0 1.0 CA A:LYS109 4.3 0.2 1.0 CB A:ASP128 4.4 0.1 1.0 NZ A:LYS109 4.5 0.9 1.0 CB A:LYS109 4.5 0.3 1.0 N A:ALA110 4.5 0.8 1.0 OG1 A:THR120 4.6 0.1 1.0 CA A:ALA110 4.6 0.2 1.0 CG A:ASP118 4.7 0.0 1.0 CD A:GLU112 4.7 0.3 1.0 NH2 A:ARG125 4.7 0.2 1.0 CB A:ASP127 4.8 0.9 1.0 CD A:LYS109 4.9 0.4 1.0 C A:ALA114 4.9 0.6 1.0 N A:ASP128 5.0 0.2 1.0

Calcium binding site 2 out of 2 in the Rat Ceruloplasmin Trigonal Form


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Rat Ceruloplasmin Trigonal Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca1107 b:0.5 occ:1.00 OD2 B:ASP128 2.0 0.9 1.0 O B:LYS109 2.6 0.2 1.0 O B:GLN124 2.8 0.8 1.0 CG B:ASP128 2.8 0.9 1.0 OD1 B:ASP128 2.9 0.5 1.0 OD2 B:ASP127 3.2 0.2 1.0 OD1 B:ASP127 3.3 0.8 1.0 OD2 B:ASP118 3.4 0.4 1.0 C B:LYS109 3.7 0.8 1.0 CG B:ASP127 3.7 0.3 1.0 OG1 B:THR120 3.7 0.8 1.0 OE1 B:GLU112 3.8 0.2 1.0 C B:GLN124 3.9 0.8 1.0 CE B:LYS109 4.1 0.1 1.0 CB B:LYS109 4.2 0.7 1.0 CB B:ASP128 4.3 0.4 1.0 O B:ALA114 4.3 0.6 1.0 CG B:ASP118 4.3 0.5 1.0 NE B:ARG125 4.4 0.4 1.0 NZ B:LYS109 4.4 0.3 1.0 CA B:LYS109 4.4 0.5 1.0 N B:ARG125 4.5 0.1 1.0 CA B:ARG125 4.5 0.2 1.0 OD1 B:ASP118 4.6 0.1 1.0 N B:ALA110 4.6 1.0 1.0 CB B:THR120 4.7 0.6 1.0 CG B:ARG125 4.8 0.9 1.0 CG2 B:THR120 4.8 0.3 1.0 CD B:LYS109 4.9 0.3 1.0 CA B:ALA110 4.9 0.0 1.0 CB B:GLU112 4.9 0.6 1.0 CA B:GLN124 4.9 0.9 1.0 CD B:ARG125 5.0 0.5 1.0

V.R.Samygina, A.V.Sokolov, G.Bourenkov, T.R.Schneider, V.A.Anashkin, S.O.Kozlov, N.N.Kolmakov, V.B.Vasilyev. Rat Ceruloplasmin: A New Labile Copper Binding Site and Zinc/Copper Mosaic. Metallomics V. 9 1828 2017.
ISSN: ESSN 1756-591X
PubMed: 29177316
DOI: 10.1039/C7MT00157F