Sodium in PDB 6qmq: Nf-Yb/C Heterodimer in Complex with Nf-Ya-Derived Peptide Stabilized with C8-Hydrocarbon Linker

The structure of Nf-Yb/C Heterodimer in Complex with Nf-Ya-Derived Peptide Stabilized with C8-Hydrocarbon Linker, PDB code: 6qmq 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)	19.89 / 2.50
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.010, 52.210, 72.990, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 27.3

The binding sites of Sodium atom in the Nf-Yb/C Heterodimer in Complex with Nf-Ya-Derived Peptide Stabilized with C8-Hydrocarbon Linker (pdb code 6qmq). 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-Derived Peptide Stabilized with C8-Hydrocarbon Linker, PDB code: 6qmq:

Sodium binding site 1 out of 1 in the Nf-Yb/C Heterodimer in Complex with Nf-Ya-Derived Peptide Stabilized with C8-Hydrocarbon Linker


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-Derived Peptide Stabilized with C8-Hydrocarbon Linker within 5.0Å range: probe atom residue distance (Å) B Occ C:Na201 b:59.9 occ:1.00 O A:ACE266 2.2 92.4 1.0 OD2 C:ASP112 2.4 72.4 1.0 OD1 C:ASP112 2.5 80.5 1.0 OD1 C:ASP109 2.6 87.9 1.0 CG C:ASP112 2.7 70.1 1.0 C A:ACE266 3.3 85.1 1.0 CG C:ASP109 3.7 88.5 1.0 N A:VAL267 4.1 86.3 1.0 CB C:ASP112 4.1 71.0 1.0 CA A:VAL267 4.2 79.1 1.0 OD2 C:ASP109 4.2 98.8 1.0 CH3 A:ACE266 4.3 71.1 1.0 O C:THR106 4.4 0.6 1.0 CB C:ASP109 4.8 63.5 1.0 CA C:ASP109 4.8 55.5 1.0 N A:ASN268 4.9 60.4 1.0 C A:VAL267 4.9 76.5 1.0

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