Sodium in PDB 3qu6: Crystal Structure of Irf-3 Dbd Free Form

The structure of Crystal Structure of Irf-3 Dbd Free Form, PDB code: 3qu6 was solved by P.E.De Ioannes, C.R.Escalante, A.K.Aggarwal, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.38 / 2.30
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	64.908, 64.908, 157.621, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 26.3

The structure of Crystal Structure of Irf-3 Dbd Free Form also contains other interesting chemical elements:

Chlorine	(Cl)	7 atoms
Zinc	(Zn)	9 atoms

The binding sites of Sodium atom in the Crystal Structure of Irf-3 Dbd Free Form (pdb code 3qu6). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of Irf-3 Dbd Free Form, PDB code: 3qu6:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Irf-3 Dbd Free Form


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 Irf-3 Dbd Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na121 b:33.2 occ:1.00 O B:HOH131 3.0 37.8 1.0 O A:HOH137 3.0 31.4 1.0 N A:GLY23 3.4 27.2 1.0 N B:GLY23 3.4 26.1 1.0 CB B:ALA25 3.7 21.8 1.0 CA B:GLY23 3.7 24.0 1.0 CA A:GLY23 3.8 23.0 1.0 O A:HOH155 3.8 30.8 1.0 O B:HOH140 3.8 35.5 1.0 CB A:ALA25 3.9 22.8 1.0 C A:GLY23 4.1 23.2 1.0 C B:GLY23 4.1 25.7 1.0 N A:VAL24 4.2 22.5 1.0 O A:LEU21 4.3 26.9 1.0 N B:VAL24 4.3 27.3 1.0 O A:VAL24 4.4 23.9 1.0 C A:GLU22 4.5 29.3 1.0 O B:LEU21 4.5 23.4 1.0 O B:VAL24 4.5 30.6 1.0 C B:GLU22 4.6 29.1 1.0 C A:VAL24 4.6 22.0 1.0 C B:VAL24 4.7 22.7 1.0 O A:GLY23 4.7 19.5 1.0 CA A:GLU22 4.7 30.1 1.0 O B:GLY23 4.8 25.9 1.0 CA B:GLU22 4.9 32.0 1.0 CA B:ALA25 4.9 21.4 1.0 CA A:ALA25 5.0 21.9 1.0 N A:ALA25 5.0 17.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Irf-3 Dbd Free Form


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 Irf-3 Dbd Free Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na122 b:25.4 occ:1.00 OD2 A:ASP50 3.1 31.7 1.0 N A:GLY52 3.2 31.6 1.0 O A:HOH140 3.3 33.6 1.0 N A:GLN55 3.3 25.7 1.0 CB A:ASP50 3.5 44.4 1.0 CA A:GLY52 3.6 34.0 1.0 C A:GLY52 3.6 29.6 1.0 CG A:ASP50 3.7 49.8 1.0 CB A:PHE54 3.7 25.6 1.0 O A:GLY52 3.7 25.6 1.0 CD1 A:LEU73 3.7 36.7 1.0 CB A:GLN55 3.8 23.0 1.0 N A:PHE54 3.8 25.2 1.0 CD2 A:PHE54 3.9 26.2 1.0 CA A:PHE54 4.1 25.7 1.0 CA A:GLN55 4.1 26.5 1.0 C A:PHE54 4.1 27.2 1.0 N A:PHE51 4.2 40.5 1.0 C A:PHE51 4.2 34.7 1.0 N A:ILE53 4.3 26.9 1.0 CG A:PHE54 4.3 29.3 1.0 CA A:PHE51 4.5 38.6 1.0 C A:ASP50 4.6 41.1 1.0 CA A:ASP50 4.7 40.5 1.0 C A:ILE53 4.8 28.6 1.0 CE3 A:TRP76 4.8 32.0 1.0 OE1 A:GLN55 4.8 30.3 1.0 OD1 A:ASP50 4.9 53.9 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Irf-3 Dbd Free Form


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of Irf-3 Dbd Free Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na117 b:22.9 occ:1.00 N B:GLN55 3.2 31.8 1.0 N B:GLY52 3.2 30.4 1.0 C B:GLY52 3.5 31.6 1.0 N B:PHE54 3.5 25.1 1.0 CA B:GLY52 3.6 30.9 1.0 O B:GLY52 3.6 23.8 1.0 CB B:PHE54 3.7 27.4 1.0 CB B:ASP50 3.7 46.6 1.0 CB B:GLN55 3.8 22.6 1.0 CD1 B:PHE54 3.8 29.3 1.0 OD2 B:ASP50 3.8 47.6 1.0 CA B:PHE54 3.9 26.6 1.0 CD1 B:LEU73 3.9 30.1 1.0 N B:ILE53 4.0 27.8 1.0 C B:PHE54 4.0 28.7 1.0 CA B:GLN55 4.1 27.1 1.0 CG B:PHE54 4.2 30.5 1.0 N B:PHE51 4.3 36.2 1.0 CG B:ASP50 4.3 54.2 1.0 C B:PHE51 4.3 34.1 1.0 C B:ILE53 4.4 23.9 1.0 CA B:PHE51 4.6 32.8 1.0 C B:ASP50 4.7 42.2 1.0 CA B:ILE53 4.8 24.4 1.0 CA B:ASP50 4.9 44.0 1.0 CE1 B:PHE54 5.0 30.6 1.0

P.De Ioannes, C.R.Escalante, A.K.Aggarwal. Structures of Apo Irf-3 and Irf-7 Dna Binding Domains: Effect of Loop L1 on Dna Binding. Nucleic Acids Res. V. 39 7300 2011.
ISSN: ISSN 0305-1048
PubMed: 21596780
DOI: 10.1093/NAR/GKR325