Sodium in PDB 9cdz: Crystal Structure of MDM2-Peptide Complex

All present enzymatic activity of Crystal Structure of MDM2-Peptide Complex:
2.3.2.27;

The structure of Crystal Structure of MDM2-Peptide Complex, PDB code: 9cdz was solved by A.K.Bera, S.Rettie, G.Bhardwaj, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.47 / 1.72
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	36.775, 48.93, 49.266, 90, 111.64, 90
R / Rfree (%)	22.2 / 27

The binding sites of Sodium atom in the Crystal Structure of MDM2-Peptide Complex (pdb code 9cdz). 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 MDM2-Peptide Complex, PDB code: 9cdz:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of MDM2-Peptide Complex


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 MDM2-Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:Na201 b:30.5 occ:1.00 NZ A:LYS93 3.0 50.3 1.0 N A:SER87 3.1 32.0 1.0 CA A:PHE86 3.7 24.8 1.0 CB A:SER87 3.7 33.0 1.0 C A:PHE86 3.8 24.3 1.0 CE A:LYS93 3.9 47.8 1.0 CA A:SER87 4.0 31.3 1.0 CG A:GLU90 4.1 42.5 0.8 CB A:PHE86 4.2 23.2 1.0 CD A:LYS93 4.5 46.3 1.0 O A:SER87 4.6 28.0 1.0 CB A:GLU90 4.6 40.0 0.8 C A:SER87 4.8 29.2 1.0 N A:PHE86 4.9 25.6 1.0 O A:SER85 4.9 29.2 1.0 OD1 D:ASP10 4.9 68.3 1.0 O A:PHE86 4.9 25.6 1.0 OG A:SER87 4.9 31.9 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of MDM2-Peptide Complex


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 MDM2-Peptide Complex within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:30.5 occ:1.00 NZ C:LYS93 3.3 42.0 1.0 N C:SER87 3.4 31.8 1.0 CA C:PHE86 3.6 32.0 1.0 CD C:LYS93 3.9 39.2 1.0 C C:PHE86 4.0 30.8 1.0 CB C:PHE86 4.0 30.0 1.0 CG C:GLU90 4.0 37.9 0.9 CE C:LYS93 4.1 39.8 1.0 CB C:SER87 4.3 34.0 1.0 CA C:SER87 4.4 31.8 1.0 CB C:GLU90 4.6 35.4 0.9 O C:SER85 4.6 35.7 1.0 N C:PHE86 4.8 32.5 1.0 O C:SER87 4.9 30.8 1.0 CD C:GLU90 5.0 39.5 0.9

S.Rettie, G.Bhardwaj. Cyclic Peptide Structure Prediction and Design Using Alphafold To Be Published.