Sodium in PDB 4p5m: Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity

The structure of Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity, PDB code: 4p5m was solved by Y.Wang, S.Dai, J.Kappler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.98 / 1.70
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	81.631, 130.468, 107.994, 90.00, 107.16, 90.00
R / Rfree (%)	16.8 / 20.4

The binding sites of Sodium atom in the Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity (pdb code 4p5m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity, PDB code: 4p5m:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:31.2 occ:1.00 O A:HOH326 2.6 25.2 1.0 N A:THR41 2.9 17.2 1.0 O A:HOH313 3.1 41.9 1.0 CA A:GLU40 3.6 20.6 1.0 CB A:THR41 3.7 17.6 1.0 OG1 A:THR41 3.7 18.1 1.0 C A:GLU40 3.7 20.4 1.0 CA A:THR41 3.9 17.8 1.0 O A:HOH472 3.9 28.3 1.0 CB A:GLU40 3.9 29.3 1.0 CB A:ALA56 4.0 15.7 1.0 O A:THR41 4.4 16.6 1.0 O A:HOH346 4.4 9.2 1.0 O A:PHE54 4.4 18.6 1.0 O A:LYS39 4.6 30.6 1.0 C A:THR41 4.6 16.4 1.0 N A:ALA56 4.7 18.3 1.0 N A:GLU40 4.8 24.7 1.0 O A:HOH309 4.9 32.2 1.0 CA A:ALA56 5.0 16.1 1.0 O A:GLU40 5.0 19.1 1.0

Sodium binding site 2 out of 2 in the Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Autoimmunity within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:32.9 occ:1.00 O C:HOH352 2.8 20.2 1.0 OE2 H:GLU135 2.8 24.7 1.0 NE2 C:GLN101 3.0 22.9 1.0 O C:HOH474 3.0 49.2 1.0 OE2 C:GLU98 3.1 35.7 0.4 CB H:GLU135 3.5 20.0 1.0 CB B:PRO86 3.8 23.9 1.0 CD H:GLU135 3.9 21.8 1.0 CG C:GLN101 3.9 17.0 1.0 CD C:GLN101 3.9 21.3 1.0 CD C:GLU98 3.9 27.3 0.4 NH2 H:ARG128 3.9 26.3 1.0 CG C:GLU98 3.9 29.7 0.6 CG C:GLU98 4.0 23.6 0.4 CG H:GLU135 4.2 20.1 1.0 CD C:GLU98 4.3 36.3 0.6 CB B:GLN90 4.3 21.1 1.0 OE2 C:GLU98 4.3 38.0 0.6 CE2 H:PHE130 4.4 17.7 1.0 O C:LEU99 4.5 16.6 0.4 O C:LEU99 4.6 15.8 0.6 N H:GLU135 4.6 16.8 1.0 CG B:PRO86 4.7 23.4 1.0 CA H:GLU135 4.7 18.9 1.0 O B:GLN90 4.8 15.0 1.0 CA B:PRO86 5.0 20.8 1.0 CG B:GLN90 5.0 22.4 1.0 OE1 H:GLU135 5.0 27.7 1.0

G.M.Clayton, Y.Wang, F.Crawford, A.Novikov, B.T.Wimberly, J.S.Kieft, M.T.Falta, N.A.Bowerman, P.Marrack, A.P.Fontenot, S.Dai, J.W.Kappler. Structural Basis of Chronic Beryllium Disease: Linking Allergic Hypersensitivity and Autoimmunity. Cell V. 158 132 2014.
ISSN: ISSN 1097-4172
PubMed: 24995984
DOI: 10.1016/J.CELL.2014.04.048