Sodium in PDB 7qdj: Racemic Structure of Pk-10 and Pk-11

The structure of Racemic Structure of Pk-10 and Pk-11, PDB code: 7qdj was solved by P.Kumar, N.G.Paterson, D.N.Woolfson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	15.70 / 1.44
Space group	C 1 2/c 1
Cell size a, b, c (Å), α, β, γ (°)	26.928, 19.379, 55.644, 90, 96.61, 90
R / Rfree (%)	13 / 16.8

The binding sites of Sodium atom in the Racemic Structure of Pk-10 and Pk-11 (pdb code 7qdj). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Racemic Structure of Pk-10 and Pk-11, PDB code: 7qdj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Racemic Structure of Pk-10 and Pk-11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Racemic Structure of Pk-10 and Pk-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na103 b:29.0 occ:0.50 O8 A:MLI101 2.0 24.0 0.4 O6 A:MLI101 3.1 17.0 0.5 C3 A:MLI101 3.1 18.4 0.3 C2 A:MLI101 3.4 15.4 0.3 C1 A:MLI101 3.7 20.3 0.5 O7 A:MLI101 4.1 13.7 0.5 O9 A:MLI101 4.2 18.2 0.2

Sodium binding site 2 out of 2 in the Racemic Structure of Pk-10 and Pk-11


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Racemic Structure of Pk-10 and Pk-11 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na104 b:28.6 occ:0.50 O A:HOH227 2.4 20.5 1.0 O A:HOH206 3.7 34.1 1.0

P.Kumar, N.G.Paterson, J.Clayden, D.N.Woolfson. De Novo Design of Discrete, Stable 3 10 -Helix Peptide Assemblies. Nature V. 607 387 2022.
ISSN: ESSN 1476-4687
PubMed: 35732733
DOI: 10.1038/S41586-022-04868-X