Sodium in PDB 3qu3: Crystal Structure of Irf-7 Dbd Apo Form

The structure of Crystal Structure of Irf-7 Dbd Apo Form, PDB code: 3qu3 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)	29.70 / 1.30
Space group	P 31
Cell size a, b, c (Å), α, β, γ (°)	68.588, 68.588, 68.610, 90.00, 90.00, 120.00
R / Rfree (%)	16.1 / 20

The binding sites of Sodium atom in the Crystal Structure of Irf-7 Dbd Apo Form (pdb code 3qu3). 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-7 Dbd Apo Form, PDB code: 3qu3:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of Irf-7 Dbd Apo 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-7 Dbd Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na135 b:28.2 occ:1.00 O A:LEU99 2.8 23.2 1.0 O A:HOH199 2.9 38.3 1.0 O A:THR102 3.2 19.4 1.0 O A:PHE105 3.2 21.1 1.0 O A:HIS100 3.5 20.5 1.0 CA A:HIS100 3.6 16.9 1.0 C A:LEU99 3.7 21.4 1.0 C A:HIS100 3.8 15.8 1.0 CB A:PHE105 3.9 15.5 1.0 CD2 A:LEU99 4.0 18.1 1.0 C A:THR102 4.0 22.3 1.0 N A:HIS100 4.1 18.1 1.0 C A:PHE105 4.2 20.3 1.0 CE1 A:TYR122 4.4 24.6 1.0 N A:THR102 4.4 20.7 1.0 CA A:PHE105 4.5 20.4 1.0 CA A:THR102 4.6 20.9 1.0 N A:PHE105 4.7 20.2 1.0 O A:HOH143 4.8 56.6 1.0 N A:SER101 4.8 17.7 1.0 N A:GLY103 4.8 29.4 1.0 CB A:THR102 4.9 17.1 1.0 CD1 A:TYR122 4.9 19.3 1.0 CB A:HIS100 4.9 17.7 1.0 CG A:PHE105 4.9 17.1 1.0 CA A:GLY103 4.9 21.9 1.0 CA A:LEU99 5.0 18.0 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of Irf-7 Dbd Apo 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-7 Dbd Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na135 b:31.1 occ:1.00 O B:PHE105 2.7 17.3 1.0 O B:LEU99 2.9 19.8 1.0 O B:HOH162 2.9 33.9 1.0 O B:THR102 2.9 22.3 1.0 O B:HOH286 3.2 34.4 1.0 CB B:PHE105 3.7 18.0 1.0 C B:PHE105 3.7 17.6 1.0 C B:THR102 3.9 26.8 1.0 O B:HIS100 4.0 23.0 1.0 C B:LEU99 4.0 20.5 1.0 CE1 B:TYR122 4.0 22.7 1.0 CA B:HIS100 4.1 20.2 1.0 CA B:PHE105 4.2 19.5 1.0 CD2 B:LEU99 4.2 24.1 1.0 C B:HIS100 4.2 18.5 1.0 N B:HIS100 4.5 25.2 1.0 N B:PHE105 4.5 20.4 1.0 CD1 B:TYR122 4.6 19.0 1.0 N B:THR102 4.6 16.9 1.0 CA B:THR102 4.7 17.4 1.0 O B:HOH179 4.7 22.8 1.0 N B:GLY103 4.7 32.2 1.0 CA B:GLY103 4.8 29.6 1.0 CG B:PHE105 4.8 19.8 1.0 CZ B:TYR122 4.9 23.3 1.0 N B:ILE106 4.9 19.3 1.0 CB B:THR102 4.9 19.7 1.0 OH B:TYR122 5.0 25.1 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of Irf-7 Dbd Apo 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-7 Dbd Apo Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na135 b:37.9 occ:1.00 O C:HOH145 2.4 27.4 1.0 O C:PHE105 2.9 19.8 1.0 O C:LEU99 3.1 16.0 1.0 O C:THR102 3.4 23.8 1.0 O C:HOH144 3.5 25.0 1.0 O C:HOH198 3.6 32.4 1.0 O C:HIS100 3.8 23.4 1.0 CA C:HIS100 3.9 20.8 1.0 C C:PHE105 4.0 19.6 1.0 C C:LEU99 4.0 18.2 1.0 CE1 C:TYR122 4.1 18.3 1.0 C C:HIS100 4.1 22.0 1.0 O C:HOH153 4.3 21.7 1.0 CB C:PHE105 4.3 22.5 1.0 N C:HIS100 4.3 18.8 1.0 CD1 C:TYR122 4.4 18.4 1.0 C C:THR102 4.4 21.6 1.0 CD1 C:LEU99 4.4 24.3 1.0 CA C:PHE105 4.6 19.6 1.0 O C:HOH187 4.6 24.0 1.0 N C:THR102 4.7 22.2 1.0 CG C:LEU99 4.8 18.9 1.0 N C:PHE105 5.0 23.1 1.0 N C:ILE106 5.0 21.8 1.0 CA C:THR102 5.0 23.0 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