Sodium in PDB 7zl7: Human Gabarap in Complex with Stapled Peptide PEN8-Ortho

The structure of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho, PDB code: 7zl7 was solved by A.Ueffing, H.Brown, D.Willbold, J.A.Kritzer, O.H.Weiergraeber, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.35 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.47, 72.42, 49.66, 90, 100.04, 90
R / Rfree (%)	17.4 / 22

The structure of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho also contains other interesting chemical elements:

Chlorine

(Cl)

8 atoms

The binding sites of Sodium atom in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho (pdb code 7zl7). 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 Human Gabarap in Complex with Stapled Peptide PEN8-Ortho, PDB code: 7zl7:

Sodium binding site 1 out of 1 in the Human Gabarap in Complex with Stapled Peptide PEN8-Ortho


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Gabarap in Complex with Stapled Peptide PEN8-Ortho within 5.0Å range: probe atom residue distance (Å) B Occ A:Na205 b:24.5 occ:1.00 O A:HOH407 2.4 31.7 1.0 O A:SER88 2.5 21.9 1.0 OE1 A:GLN93 2.5 17.7 1.0 O A:HOH339 2.7 20.4 1.0 CD A:GLN93 3.4 14.6 1.0 C A:SER88 3.5 23.9 1.0 NE2 A:GLN93 3.6 20.7 1.0 CA A:ALA89 3.8 18.1 1.0 O A:HOH395 4.0 34.0 1.0 N A:ALA89 4.1 15.9 1.0 O A:HOH402 4.2 37.0 1.0 OG A:SER88 4.4 20.9 1.0 CB A:SER88 4.4 21.1 1.0 CA A:SER88 4.6 22.7 1.0 N A:THR90 4.6 14.2 1.0 C A:ALA89 4.6 19.8 1.0 CG A:GLN93 4.8 16.6 1.0 CB A:ALA89 4.8 16.8 1.0 O A:HOH438 5.0 43.0 1.0

H.Brown, M.Chung, A.Uffing, N.Batistatou, T.Tsang, S.Doskocil, W.Mao, D.Willbold, R.C.Bast Jr., Z.Lu, O.H.Weiergraber, J.A.Kritzer. Structure-Based Design of Stapled Peptides That Bind Gabarap and Inhibit Autophagy. J.Am.Chem.Soc. V. 144 14687 2022.
ISSN: ESSN 1520-5126
PubMed: 35917476
DOI: 10.1021/JACS.2C04699