Sodium in PDB 8ru4: Crystal Structure of Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor

The structure of Crystal Structure of Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor, PDB code: 8ru4 was solved by A.Yeste Vazquez, C.I.R.Klintrot, T.N.Grossmann, S.Hennig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.96 / 2.13
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	64.567, 103.617, 187.923, 90, 90, 90
R / Rfree (%)	20.1 / 24

The structure of Crystal Structure of Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor (pdb code 8ru4). 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 Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor, PDB code: 8ru4:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor


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 Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ A:Na707 b:54.3 occ:1.00 O A:HOH930 2.3 45.0 1.0 O A:HOH903 2.6 42.2 1.0 NE A:ARG474 3.7 33.0 1.0 OG A:SER473 3.9 39.2 1.0 NH2 A:ARG474 4.3 41.7 1.0 O A:HOH859 4.4 31.9 1.0 CB A:SER473 4.4 33.2 1.0 CZ A:ARG474 4.5 33.4 1.0 OD1 A:ASN516 4.5 28.3 1.0 CD A:ARG474 4.6 27.3 1.0 NH1 A:ARG515 4.6 37.3 1.0 ND2 A:ASN516 4.9 34.0 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor


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 Human Catenin Beta-1 in Complex with Stitched Peptide Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ B:Na707 b:52.7 occ:1.00 OG1 B:THR371 2.4 39.0 1.0 O B:HOH957 2.6 36.2 1.0 O B:LEU368 2.7 36.5 1.0 O B:HOH904 2.8 44.3 1.0 N B:THR371 3.2 38.0 1.0 CB B:THR371 3.5 36.4 1.0 CA B:THR371 3.6 39.0 1.0 C B:THR371 3.6 39.5 1.0 N B:ASP372 3.6 34.3 1.0 C B:LEU368 3.7 23.9 1.0 CA B:HIS369 3.8 30.1 1.0 N B:LEU370 3.9 27.8 1.0 C B:HIS369 3.9 28.6 1.0 N B:HIS369 4.1 27.6 1.0 O B:THR371 4.3 45.3 1.0 C B:LEU370 4.3 29.5 1.0 CG2 B:THR371 4.4 35.5 1.0 O B:HOH834 4.4 30.7 1.0 CA B:ASP372 4.5 36.0 1.0 O B:HIS369 4.5 27.6 1.0 CA B:LEU370 4.7 31.2 1.0 CB B:ASP372 4.9 40.3 1.0 CA B:LEU368 4.9 29.1 1.0

A.Yeste-Vazquez, F.M.Paulussen, M.Wendt, R.Klintrot, C.Schulte, K.Wallraven, L.Van Gijzel, B.Simeonov, M.Van Der Gaag, A.Gerber, H.M.Maric, S.Hennig, T.N.Grossmann. Structure-Based Design of Bicyclic Helical Peptides That Target the Oncogene Beta-Catenin. Angew.Chem.Int.Ed.Engl. 11749 2024.
ISSN: ESSN 1521-3773
PubMed: 39167026
DOI: 10.1002/ANIE.202411749