Sodium in PDB 7q3z: Dna/Rna Binding Protein

Protein crystallography data

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

Other elements in 7q3z:

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

Zinc (Zn) 2 atoms

Sodium Binding Sites:

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 7q3z

Go back to Sodium Binding Sites List in 7q3z
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 7q3z

Go back to Sodium Binding Sites List in 7q3z
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

Reference:

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
Page generated: Fri Apr 7 15:40:56 2023

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