Sodium in PDB 7ygi: Crystal Structure of P53 Dbd Domain in Complex with Azurin

The structure of Crystal Structure of P53 Dbd Domain in Complex with Azurin, PDB code: 7ygi was solved by W.X.Jiang, J.Q.Zuo, J.J.Hu, X.Q.Chen, L.X.Ma, Z.Liu, Q.Xing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.88 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	144.839, 68.75, 83.847, 90, 99.69, 90
R / Rfree (%)	21.3 / 27

The structure of Crystal Structure of P53 Dbd Domain in Complex with Azurin also contains other interesting chemical elements:

Zinc	(Zn)	2 atoms
Potassium	(K)	2 atoms

The binding sites of Sodium atom in the Crystal Structure of P53 Dbd Domain in Complex with Azurin (pdb code 7ygi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of P53 Dbd Domain in Complex with Azurin, PDB code: 7ygi:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of P53 Dbd Domain in Complex with Azurin


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 P53 Dbd Domain in Complex with Azurin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:37.7 occ:1.00 OE1 A:GLN165 2.6 33.7 1.0 N A:GLN165 2.7 20.3 1.0 CB A:GLN165 2.7 27.9 1.0 CG A:GLN165 2.9 33.4 1.0 CD A:GLN165 3.1 39.8 1.0 CA A:GLN165 3.2 22.8 1.0 O A:PRO250 3.5 28.7 1.0 N A:LYS164 3.5 18.4 1.0 CD2 A:HIS168 3.6 28.0 1.0 C A:LYS164 3.8 16.0 1.0 CB A:TYR163 3.8 19.2 1.0 CD A:PRO250 3.9 19.1 1.0 CB A:HIS168 4.0 26.2 1.0 CG A:PRO250 4.0 20.7 1.0 O A:GLN165 4.0 31.2 1.0 CB A:ARG249 4.0 21.4 1.0 C A:GLN165 4.1 26.2 1.0 CA A:LYS164 4.1 15.0 1.0 CG A:HIS168 4.1 27.3 1.0 C A:TYR163 4.1 23.8 1.0 N A:PRO250 4.2 26.6 1.0 CD1 A:TYR163 4.3 15.4 1.0 CA A:TYR163 4.4 24.9 1.0 NE2 A:GLN165 4.4 45.7 1.0 C A:PRO250 4.4 17.6 1.0 CB A:LYS164 4.5 19.6 1.0 CG A:TYR163 4.5 26.6 1.0 CG A:ARG249 4.6 22.4 1.0 C A:ARG249 4.7 28.0 1.0 NE2 A:HIS168 4.8 28.2 1.0 CA A:PRO250 4.8 20.7 1.0 CA A:ARG249 4.8 25.9 1.0 O A:LYS164 4.8 17.8 1.0 CB A:PRO250 4.9 25.1 1.0 O A:TYR163 4.9 16.6 1.0 CD A:ARG249 4.9 23.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of P53 Dbd Domain in Complex with Azurin


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 P53 Dbd Domain in Complex with Azurin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:27.7 occ:1.00 OH B:TYR205 2.5 23.2 1.0 OD2 B:ASP186 2.8 46.5 1.0 O B:VAL197 2.9 18.0 1.0 CZ B:TYR205 3.5 20.3 1.0 O B:HOH480 3.6 23.0 1.0 CE1 B:TYR205 3.6 15.1 1.0 CG1 B:VAL203 3.6 16.8 1.0 CG B:ASP186 3.8 43.6 1.0 N B:VAL197 3.9 15.6 1.0 C B:VAL197 4.0 16.8 1.0 OD1 B:ASP186 4.0 45.7 1.0 CB B:LEU188 4.0 20.0 1.0 CD1 B:LEU188 4.2 17.4 1.0 CB B:ARG196 4.3 18.7 1.0 CG2 B:VAL203 4.4 13.1 1.0 N B:ALA189 4.4 21.8 1.0 CB B:VAL203 4.5 14.2 1.0 CB B:ALA189 4.5 30.0 1.0 CA B:VAL197 4.5 13.7 1.0 CG B:LEU188 4.7 19.4 1.0 CE2 B:TYR205 4.8 15.5 1.0 CD B:ARG196 4.8 29.6 1.0 CA B:ARG196 4.8 14.0 1.0 C B:ARG196 4.8 19.7 1.0 CG B:ARG196 4.9 16.4 1.0 CA B:ALA189 4.9 32.1 1.0 CD1 B:TYR205 5.0 19.4 1.0

J.Hu, W.Jiang, J.Zuo, D.Shi, X.Chen, X.Yang, W.Zhang, L.Ma, Z.Liu, Q.Xing. Structural Basis of Bacterial Effector Protein Azurin Targeting Tumor Suppressor P53 and Inhibiting Its Ubiquitination. Commun Biol V. 6 59 2023.
ISSN: ESSN 2399-3642
PubMed: 36650277
DOI: 10.1038/S42003-023-04458-1