Sodium in PDB 5tj4: Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein

The structure of Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein, PDB code: 5tj4 was solved by L.K.Chao, O.Herzberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	173.04 / 3.50
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	89.599, 274.569, 174.019, 90.00, 96.09, 90.00
R / Rfree (%)	21.3 / 24.9

The binding sites of Sodium atom in the Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein (pdb code 5tj4). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein, PDB code: 5tj4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1502 b:51.0 occ:1.00 O B:ALA1403 2.3 55.6 1.0 O C:LYS29 2.5 54.1 1.0 O B:GLU1401 2.6 62.4 1.0 O B:LEU1400 2.9 51.9 1.0 C B:GLU1401 3.4 61.2 1.0 C C:LYS29 3.4 51.1 1.0 C B:ALA1403 3.5 54.1 1.0 O C:GLU28 3.5 57.5 1.0 CA C:LYS29 3.9 52.4 1.0 NH2 B:ARG1268 3.9 0.7 1.0 N B:ALA1403 3.9 50.9 1.0 C B:LEU1400 4.0 56.5 1.0 CA B:GLU1401 4.0 68.0 1.0 C B:LEU1402 4.1 47.0 1.0 CA C:GLY32 4.1 71.6 1.0 N C:GLY32 4.2 68.9 1.0 CA B:ALA1403 4.2 55.1 1.0 N B:LEU1402 4.3 54.7 1.0 O B:LEU1402 4.3 46.5 1.0 N B:GLU1404 4.4 52.9 1.0 N B:GLU1401 4.4 61.0 1.0 C C:GLU28 4.5 62.5 1.0 N C:ASP30 4.5 50.5 1.0 CA B:LEU1402 4.7 48.1 1.0 O C:ASP30 4.7 63.6 1.0 CA B:GLU1404 4.7 58.5 1.0 N C:LYS29 4.7 57.6 1.0 C C:ASP30 4.8 57.6 1.0 CZ B:ARG1268 4.9 0.6 1.0 CB B:ALA1403 5.0 60.7 1.0 CA C:ASP30 5.0 53.8 1.0

Sodium binding site 2 out of 2 in the Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Gasdermin-B C-Terminal Domain Containing the Polymorphism Residues GLY299:PRO306 Fused to Maltose Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1502 b:59.6 occ:1.00 O E:ALA1403 2.3 63.7 1.0 O E:GLU1401 2.5 66.4 1.0 O A:LYS29 2.8 60.8 1.0 O E:LEU1400 3.3 48.9 1.0 C E:GLU1401 3.4 58.7 1.0 C E:ALA1403 3.4 53.6 1.0 C A:LYS29 3.7 59.4 1.0 NH1 E:ARG1268 3.7 0.9 1.0 CA A:LYS29 3.8 66.0 1.0 O A:GLU28 3.8 61.1 1.0 C E:LEU1402 3.9 46.5 1.0 N E:ALA1403 3.9 43.7 1.0 O E:LEU1402 4.0 50.7 1.0 CA E:GLU1401 4.2 62.3 1.0 CA E:ALA1403 4.2 46.9 1.0 N E:LEU1402 4.3 52.9 1.0 C E:LEU1400 4.3 51.4 1.0 N E:GLU1404 4.4 55.1 1.0 CA E:LEU1402 4.5 50.7 1.0 CG E:GLU1404 4.5 72.1 1.0 CZ E:ARG1268 4.5 0.0 1.0 NH2 E:ARG1268 4.6 0.7 1.0 CA E:GLU1404 4.6 61.1 1.0 C A:GLU28 4.6 67.2 1.0 N A:LYS29 4.7 66.8 1.0 N E:GLU1401 4.8 54.4 1.0 CB A:LYS29 4.8 71.0 1.0 CA A:GLY32 4.8 50.3 1.0 N A:ASP30 4.9 51.5 1.0 OE2 E:GLU1401 4.9 0.4 1.0

K.L.Chao, L.Kulakova, O.Herzberg. Gene Polymorphism Linked to Increased Asthma and Ibd Risk Alters Gasdermin-B Structure, A Sulfatide and Phosphoinositide Binding Protein. Proc. Natl. Acad. Sci. V. 114 E1128 2017U.S.A..
ISSN: ESSN 1091-6490
PubMed: 28154144
DOI: 10.1073/PNAS.1616783114