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

Protein crystallography data

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

Other elements in 3tlr:

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

Cadmium (Cd) 10 atoms

Sodium Binding Sites:

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 3tlr

Go back to Sodium Binding Sites List in 3tlr
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 3tlr

Go back to Sodium Binding Sites List in 3tlr
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

Reference:

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
Page generated: Tue Dec 15 06:26:22 2020

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