Sodium in PDB 3tlr: Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant

The structure of Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant, PDB code: 3tlr was solved by M.Colombo, S.Ricagno, M.Bolognesi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.92 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	29.930, 98.200, 142.380, 90.00, 90.00, 90.00
R / Rfree (%)	22.5 / 26.6

The structure of Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant also contains other interesting chemical elements:

Cadmium

(Cd)

10 atoms

The binding sites of Sodium atom in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant (pdb code 3tlr). 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 the Tetrameric Beta-2 Microglobulin DIMC20 Mutant, PDB code: 3tlr:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 the Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:83.4 occ:1.00 OD1 A:ASP96 3.4 56.5 1.0 OD2 A:ASP96 3.5 66.9 1.0 CB A:ASP98 3.7 46.4 1.0 CG A:ASP96 3.8 56.8 1.0 OD1 A:ASP98 4.1 56.2 0.1 C A:ASP98 4.3 49.9 1.0 CG A:ASP98 4.4 55.8 0.1 CA A:ASP98 4.5 44.6 1.0 O A:ASP98 4.6 49.1 1.0 N A:MET99 4.6 47.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Tetrameric Beta-2 Microglobulin DIMC20 Mutant


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 the Tetrameric Beta-2 Microglobulin DIMC20 Mutant within 5.0Å range: probe atom residue distance (Å) B Occ B:Na104 b:45.5 occ:1.00 OD1 B:ASP96 2.4 63.4 1.0 OD2 B:ASP96 2.6 70.8 1.0 CG B:ASP96 2.8 63.0 1.0 OD2 B:ASP98 3.4 82.1 1.0 CB B:ASP98 3.6 59.9 1.0 CG B:ASP98 3.8 74.3 1.0 CB B:ASP96 4.3 49.8 1.0 CA B:ASP98 4.5 57.6 1.0 N B:ASP98 4.7 56.9 1.0 N B:MET99 4.7 60.3 1.0 C B:ASP98 4.8 62.9 1.0 OD1 B:ASP98 4.8 75.1 1.0

M.Colombo, M.De Rosa, V.Bellotti, S.Ricagno, M.Bolognesi. A Recurrent D-Strand Association Interface Is Observed in Beta-2 Microglobulin Oligomers. Febs J. V. 279 1131 2012.
ISSN: ISSN 1742-464X
PubMed: 22289140
DOI: 10.1111/J.1742-4658.2012.08510.X