Sodium in PDB 5n0k: Rat Ceruloplasmin Orthorhombic Form

The structure of Rat Ceruloplasmin Orthorhombic Form, PDB code: 5n0k 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)	14.98 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.360, 103.810, 172.811, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 22.6

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

Copper	(Cu)	9 atoms
Calcium	(Ca)	1 atom

The binding sites of Sodium atom in the Rat Ceruloplasmin Orthorhombic Form (pdb code 5n0k). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Rat Ceruloplasmin Orthorhombic Form, PDB code: 5n0k:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1112 b:54.2 occ:1.00 O A:SER236 2.4 44.6 1.0 O A:TYR36 2.4 46.8 1.0 O A:GLY45 2.4 59.0 1.0 OH A:TYR48 2.5 41.0 1.0 O A:HOH1375 2.6 45.5 1.0 C A:GLY45 3.5 60.0 1.0 C A:TYR36 3.5 47.7 1.0 C A:SER236 3.5 45.2 1.0 SD A:MET239 3.6 44.7 1.0 CZ A:TYR48 3.6 41.8 1.0 CE1 A:TYR48 3.9 41.9 1.0 N A:GLY45 4.0 62.3 1.0 CA A:GLY45 4.0 61.7 1.0 CA A:TYR36 4.1 45.1 1.0 CE A:MET239 4.1 44.5 1.0 O A:HOH1304 4.2 48.7 1.0 N A:ASN237 4.4 45.0 1.0 CA A:ASN237 4.4 45.7 1.0 OD1 A:ASN237 4.5 52.4 1.0 CA A:SER236 4.5 45.7 1.0 CB A:SER236 4.5 47.4 1.0 N A:LEU37 4.6 52.1 1.0 N A:ARG46 4.6 59.3 1.0 CB A:TYR36 4.8 43.8 1.0 OG A:SER236 4.9 48.3 1.0 CE2 A:TYR48 4.9 42.1 1.0 CA A:LEU37 4.9 56.1 1.0 CA A:ARG46 4.9 58.1 1.0

Sodium binding site 2 out of 2 in the Rat Ceruloplasmin Orthorhombic Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Rat Ceruloplasmin Orthorhombic Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1113 b:25.4 occ:1.00 SG A:CYS220 1.9 67.5 1.0 O A:ASP42 2.5 69.0 1.0 CB A:CYS220 3.2 77.3 1.0 CG2 A:VAL226 3.3 0.6 1.0 CB A:VAL226 3.4 0.3 1.0 C A:ASP42 3.4 75.0 1.0 CE1 A:PHE233 3.6 50.1 1.0 CG1 A:VAL226 3.7 0.5 1.0 CA A:ASP42 4.0 77.6 1.0 CZ A:PHE233 4.0 51.0 1.0 CG2 A:ILE216 4.1 64.9 1.0 CD1 A:PHE233 4.2 50.8 1.0 CG1 A:ILE216 4.3 61.5 1.0 N A:ARG43 4.4 73.5 1.0 CA A:CYS220 4.6 79.6 1.0 O A:PRO41 4.7 85.2 1.0 CB A:ILE216 4.7 63.6 1.0 CD1 A:ILE216 4.8 59.4 1.0 CB A:ASP42 4.8 77.0 1.0 CA A:VAL226 4.8 1.0 1.0 CA A:ARG43 4.9 70.3 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