Sodium in PDB 5o6n: High Pressure Flash Cooled Concanavalin A

The structure of High Pressure Flash Cooled Concanavalin A, PDB code: 5o6n was solved by Y.Thielmann, D.Quirnheim Pais, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	33.23 / 1.35
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	61.260, 86.230, 89.020, 90.00, 90.00, 90.00
R / Rfree (%)	13.3 / 16.4

The structure of High Pressure Flash Cooled Concanavalin A also contains other interesting chemical elements:

Manganese	(Mn)	1 atom
Calcium	(Ca)	1 atom
Chlorine	(Cl)	2 atoms

The binding sites of Sodium atom in the High Pressure Flash Cooled Concanavalin A (pdb code 5o6n). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the High Pressure Flash Cooled Concanavalin A, PDB code: 5o6n:

Sodium binding site 1 out of 1 in the High Pressure Flash Cooled Concanavalin A


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Pressure Flash Cooled Concanavalin A within 5.0Å range: probe atom residue distance (Å) B Occ A:Na303 b:24.6 occ:0.86 O A:LYS46 2.6 17.1 1.0 OH A:TYR67 3.0 20.9 1.0 O A:GLN43 3.0 18.2 1.0 CE A:MET42 3.2 18.5 0.3 N A:ILE199 3.2 12.6 1.0 O A:ILE199 3.2 14.4 1.0 CE1 A:TYR67 3.6 15.1 1.0 CB A:ILE199 3.7 12.5 1.0 C A:LYS46 3.7 14.7 1.0 CZ A:TYR67 3.8 18.1 1.0 CA A:ILE199 3.8 12.0 1.0 N A:LYS46 3.9 15.3 1.0 CE2 A:PHE197 3.9 13.4 1.0 C A:ILE199 3.9 12.9 1.0 C A:GLN43 4.1 17.2 1.0 CD2 A:PHE197 4.1 12.4 1.0 C A:LEU198 4.2 13.3 1.0 N A:GLY45 4.3 15.5 1.0 CA A:LYS46 4.3 15.1 0.2 CA A:LYS46 4.4 15.4 0.5 CA A:LEU198 4.4 13.0 1.0 CA A:LYS46 4.4 15.6 0.3 CG1 A:ILE199 4.5 12.8 1.0 O A:PHE197 4.5 13.5 1.0 CD1 A:LEU198 4.7 21.5 1.0 CE A:MET42 4.7 12.7 0.4 SD A:MET42 4.7 18.2 0.3 CB A:LYS46 4.8 15.0 0.2 C A:GLY45 4.8 17.5 1.0 N A:VAL47 4.8 13.7 1.0 N A:GLY48 4.8 11.8 1.0 CB A:LYS46 4.8 15.7 0.5 CD1 A:ILE199 4.8 14.0 1.0 N A:GLN43 4.9 14.9 1.0 CG2 A:ILE199 4.9 13.0 1.0 CD1 A:TYR67 4.9 14.0 1.0 CB A:LYS46 4.9 16.6 0.3 CA A:ASN44 4.9 17.0 1.0 C A:ASN44 4.9 17.0 1.0 N A:ASN44 4.9 16.4 1.0 CG A:MET42 5.0 17.2 0.3 CG A:MET42 5.0 13.8 0.4

D.Quirnheim Pais, B.Rathmann, J.Koepke, C.Tomova, P.Wurzinger, Y.Thielmann. A Standardized Technique For High-Pressure Cooling of Protein Crystals. Acta Crystallogr D Struct V. 73 997 2017BIOL.
ISSN: ISSN 2059-7983
PubMed: 29199979
DOI: 10.1107/S2059798317016357