Sodium in PDB 5m6i: Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8

The structure of Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8, PDB code: 5m6i was solved by L.Oberti, P.Rognoni, R.Russo, J.Bacarizo, M.Bolognesi, S.Ricagno, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	54.56 / 2.20
Space group	I 4 2 2
Cell size a, b, c (Å), α, β, γ (°)	229.378, 229.378, 64.429, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 22.7

The binding sites of Sodium atom in the Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8 (pdb code 5m6i). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8, PDB code: 5m6i:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:30.8 occ:1.00 NE2 A:GLN188 3.3 34.4 1.0 O A:HOH480 3.5 28.4 1.0 NE2 A:HIS192 3.6 26.1 1.0 CG A:GLN188 3.6 23.1 1.0 CD A:GLN188 4.0 32.0 1.0 CB A:GLN188 4.1 24.1 1.0 O A:HOH497 4.2 29.8 1.0 CD2 A:HIS192 4.4 22.6 1.0 CE1 A:HIS192 4.5 25.3 1.0 CA A:GLN188 4.6 25.2 1.0 OG A:SER191 4.7 28.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Non-Cardiotoxic Bence-Jones Light Chain Dimer M8 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:30.0 occ:1.00 OG A:SER196 3.0 31.5 1.0 OG A:SER194 3.0 52.1 1.0 N A:GLY156 3.2 28.5 1.0 N A:ASP155 3.5 20.5 1.0 CB A:SER196 3.5 20.4 1.0 N A:SER196 3.5 22.5 1.0 O A:LYS153 3.6 25.7 1.0 C A:SER194 3.7 21.0 1.0 C A:TYR195 3.7 26.8 1.0 O A:SER194 3.7 20.5 1.0 CB A:SER194 3.7 17.4 1.0 C A:LYS153 3.7 21.3 1.0 CA A:TYR195 3.7 21.1 1.0 N A:TYR195 3.7 23.5 1.0 CB A:LYS153 3.8 21.4 1.0 CA A:GLY156 3.9 22.6 1.0 CA A:ALA154 4.0 19.2 1.0 N A:ALA154 4.0 20.4 1.0 C A:ALA154 4.0 20.7 1.0 CA A:SER196 4.1 18.2 1.0 C A:ASP155 4.1 26.2 1.0 CA A:ASP155 4.1 23.7 1.0 CA A:SER194 4.3 23.0 1.0 O A:TYR195 4.3 23.4 1.0 CA A:LYS153 4.4 20.3 1.0 CG2 A:THR209 4.8 31.0 1.0 O A:ALA154 4.9 29.9 1.0 C A:GLY156 5.0 24.2 1.0

L.Oberti, P.Rognoni, A.Barbiroli, F.Lavatelli, R.Russo, M.Maritan, G.Palladini, M.Bolognesi, G.Merlini, S.Ricagno. Concurrent Structural and Biophysical Traits Link with Immunoglobulin Light Chains Amyloid Propensity. Sci Rep V. 7 16809 2017.
ISSN: ESSN 2045-2322
PubMed: 29196671
DOI: 10.1038/S41598-017-16953-7