Sodium in PDB 6qmp: Nf-Yb/C Heterodimer in Complex with Nf-Ya Peptide

The structure of Nf-Yb/C Heterodimer in Complex with Nf-Ya Peptide, PDB code: 6qmp was solved by S.Kiehstaller, S.Jeganathan, M.Wendt, T.N.Grossmann, S.Hennig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.91 / 2.00
Space group	P 32 2 1
Cell size a, b, c (Å), α, β, γ (°)	52.900, 52.900, 134.100, 90.00, 90.00, 120.00
R / Rfree (%)	21.3 / 27.3

The binding sites of Sodium atom in the Nf-Yb/C Heterodimer in Complex with Nf-Ya Peptide (pdb code 6qmp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Nf-Yb/C Heterodimer in Complex with Nf-Ya Peptide, PDB code: 6qmp:

Sodium binding site 1 out of 1 in the Nf-Yb/C Heterodimer in Complex with Nf-Ya Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Nf-Yb/C Heterodimer in Complex with Nf-Ya Peptide within 5.0Å range: probe atom residue distance (Å) B Occ C:Na202 b:91.0 occ:1.00 O C:THR106 3.3 59.0 1.0 OD1 C:ASP109 3.3 81.4 0.3 C C:THR106 4.4 53.5 1.0 OD1 C:ASP112 4.5 86.5 1.0 CG C:ASP109 4.5 78.2 0.3 N C:PHE108 4.8 52.7 1.0 N C:ASP109 4.9 63.1 1.0 C C:LYS107 5.0 63.9 1.0 CA C:ASP109 5.0 68.5 0.7 CA C:ASP109 5.0 67.8 0.3

S.Jeganathan, M.Wendt, S.Kiehstaller, D.Brancaccio, A.Kuepper, N.Pospiech, A.Carotenuto, E.Novellino, S.Hennig, T.N.Grossmann. Constrained Peptides with Fine-Tuned Flexibility Inhibit Nf-Y Transcription Factor Assembly. Angew.Chem.Int.Ed.Engl. V. 58 17351 2019.
ISSN: ESSN 1521-3773
PubMed: 31539186
DOI: 10.1002/ANIE.201907901