Sodium in PDB 7q3z: Dna/Rna Binding Protein

The structure of Dna/Rna Binding Protein, PDB code: 7q3z was solved by E.Huber, K.Lammens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.90 / 1.85
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	49.88, 64.04, 104.58, 90, 93, 90
R / Rfree (%)	18.8 / 21.3

The structure of Dna/Rna Binding Protein also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Dna/Rna Binding Protein (pdb code 7q3z). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Dna/Rna Binding Protein, PDB code: 7q3z:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Dna/Rna Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dna/Rna Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:53.4 occ:1.00 OD2 B:ASP177 2.6 32.3 1.0 O B:ALA173 3.0 23.8 1.0 CG B:ASP177 3.0 39.3 1.0 CB B:ASP177 3.1 40.3 1.0 CD2 B:PHE176 3.4 20.6 1.0 N B:ASP177 3.7 21.0 1.0 CA B:ASP177 3.9 33.9 1.0 C B:ALA173 3.9 24.9 1.0 OD1 B:ASP177 4.0 35.1 1.0 CB B:PHE176 4.1 21.6 1.0 CG B:PHE176 4.2 22.8 1.0 CE2 B:PHE176 4.3 26.4 1.0 C B:PHE176 4.3 20.1 1.0 CA B:ALA173 4.3 24.5 1.0 CB B:ALA173 4.6 22.5 1.0 CA B:PHE176 4.7 22.4 1.0

Sodium binding site 2 out of 2 in the Dna/Rna Binding Protein


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Dna/Rna Binding Protein within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:70.8 occ:1.00 OD2 A:ASP177 2.2 40.6 1.0 O A:ALA173 2.6 21.3 1.0 CG A:ASP177 2.7 40.8 1.0 CB A:ASP177 3.1 46.0 1.0 OD1 A:ASP177 3.5 36.0 1.0 C A:ALA173 3.6 23.5 1.0 N A:ASP177 3.7 26.1 1.0 CA A:ASP177 4.0 38.8 1.0 CD2 A:PHE176 4.1 23.9 1.0 CA A:ALA173 4.2 27.4 1.0 CB A:ALA173 4.3 23.5 1.0 CB A:PHE176 4.4 18.5 1.0 C A:PHE176 4.6 23.1 1.0 N A:ALA174 4.6 22.7 1.0 CG A:PHE176 4.8 18.1 1.0 CA A:ALA174 4.9 24.2 1.0 CA A:PHE176 4.9 18.6 1.0

F.J.Metzner, E.Huber, K.P.Hopfner, K.Lammens. Structural and Biochemical Characterization of Human Schlafen 5. Nucleic Acids Res. V. 50 1147 2022.
ISSN: ESSN 1362-4962
PubMed: 35037067
DOI: 10.1093/NAR/GKAB1278