Sodium in PDB 4p4k: Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Auto Immunity

The structure of Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Auto Immunity, PDB code: 4p4k was solved by G.M.Clayton, F.Crawford, J.W.Kappler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.70 / 2.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	79.400, 137.240, 213.130, 90.00, 90.00, 90.00
R / Rfree (%)	20.4 / 25.2

The binding sites of Sodium atom in the Structural Basis of Chronic Beryllium Disease: Bridging the Gap Between Allergic Hypersensitivity and Auto Immunity (pdb code 4p4k). 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 Auto Immunity, PDB code: 4p4k:
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 Auto Immunity


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 Auto Immunity within 5.0Å range: probe atom residue distance (Å) B Occ B:Na202 b:63.6 occ:1.00 OE1 B:GLU-17 2.1 68.1 1.0 OE2 B:GLU69 2.7 63.5 1.0 O B:HOH344 2.7 52.8 1.0 BE B:0BE203 2.7 17.1 1.0 OD2 B:ASP-20 2.8 64.1 1.0 OE1 B:GLU69 3.0 50.2 1.0 OE2 B:GLU68 3.0 49.6 1.0 OD1 B:ASP-20 3.0 51.6 1.0 CD B:GLU69 3.1 60.7 1.0 CD B:GLU-17 3.2 59.4 1.0 CG B:ASP-20 3.3 52.4 1.0 O B:LEU-19 3.4 40.6 1.0 OE2 B:GLU-17 3.6 42.5 1.0 CD B:GLU68 4.1 54.8 1.0 OE1 B:GLU26 4.3 58.9 1.0 CG B:GLU69 4.4 42.1 1.0 CG B:GLU-17 4.4 42.7 1.0 O B:HOH331 4.5 45.4 1.0 C B:LEU-19 4.5 41.7 1.0 N B:GLU69 4.5 36.8 1.0 CG B:GLU68 4.5 43.7 1.0 CA B:GLU69 4.6 35.9 1.0 CB B:GLU68 4.7 39.8 1.0 CB B:GLU69 4.7 36.9 1.0 C B:GLU68 4.7 42.3 1.0 O B:GLU68 4.8 42.4 1.0 CB B:ASP-20 4.8 41.3 1.0 N B:LEU-19 4.8 38.4 1.0 OE2 B:GLU26 4.9 60.2 1.0

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


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 Auto Immunity within 5.0Å range: probe atom residue distance (Å) B Occ F:Na201 b:52.8 occ:1.00 OE1 F:GLU-17 2.2 70.0 1.0 BE F:0BE202 2.7 18.1 1.0 OE2 F:GLU69 2.7 44.6 1.0 OE2 F:GLU68 2.8 51.6 1.0 OD2 F:ASP-20 3.1 55.1 1.0 OE1 F:GLU69 3.2 51.2 1.0 CD F:GLU69 3.2 50.6 1.0 OD1 F:ASP-20 3.3 46.5 1.0 CD F:GLU-17 3.3 59.1 1.0 CG F:ASP-20 3.6 47.4 1.0 O F:LEU-19 3.7 41.2 1.0 CD F:GLU68 3.7 54.4 1.0 OE2 F:GLU-17 3.7 31.0 1.0 CG F:GLU68 3.8 40.0 1.0 O F:HOH349 4.1 35.1 1.0 N F:GLU69 4.2 35.8 1.0 CA F:GLU69 4.3 34.5 1.0 O F:HOH315 4.3 32.6 1.0 CB F:GLU68 4.4 36.5 1.0 CG F:GLU69 4.4 38.9 1.0 C F:GLU68 4.5 40.4 1.0 CB F:GLU69 4.6 35.2 1.0 OE1 F:GLU26 4.6 51.4 1.0 CG F:GLU-17 4.6 46.4 1.0 C F:LEU-19 4.8 40.3 1.0 O F:GLU68 4.8 41.4 1.0 OE1 F:GLU68 4.9 40.6 1.0 O F:ILE65 4.9 41.7 1.0 CG2 F:VAL72 4.9 40.3 1.0 N F:LEU-19 5.0 37.0 1.0 OE2 F:GLU26 5.0 45.8 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