Sodium in PDB 6hhd: Mouse Prion Protein in Complex with Nanobody 484

The structure of Mouse Prion Protein in Complex with Nanobody 484, PDB code: 6hhd was solved by S.Soror, R.Abskharon, A.Wohlkonig, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	57.85 / 2.10
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	59.130, 63.798, 69.792, 90.00, 101.96, 90.00
R / Rfree (%)	20.6 / 24.5

The structure of Mouse Prion Protein in Complex with Nanobody 484 also contains other interesting chemical elements:

Chlorine

(Cl)

3 atoms

The binding sites of Sodium atom in the Mouse Prion Protein in Complex with Nanobody 484 (pdb code 6hhd). 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 Mouse Prion Protein in Complex with Nanobody 484, PDB code: 6hhd:

Sodium binding site 1 out of 1 in the Mouse Prion Protein in Complex with Nanobody 484


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Mouse Prion Protein in Complex with Nanobody 484 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na303 b:32.5 occ:1.00 HH11 C:ARG164 2.2 34.1 1.0 O D:HOH310 2.5 21.7 1.0 HA3 D:GLY109 2.7 27.6 1.0 HE22 C:GLN168 2.9 24.2 1.0 NH1 C:ARG164 3.0 28.4 1.0 HH12 C:ARG164 3.1 34.1 1.0 HA2 D:GLY109 3.3 27.6 1.0 NE2 C:GLN168 3.4 20.2 1.0 CA D:GLY109 3.4 23.0 1.0 HE21 C:GLN168 3.8 24.2 1.0 O D:GLY109 3.8 24.7 1.0 OE1 C:GLN168 3.9 21.9 1.0 CD C:GLN168 3.9 19.5 1.0 HE C:ARG164 4.0 30.1 1.0 C D:GLY109 4.1 23.4 1.0 CZ C:ARG164 4.1 26.3 1.0 O D:HOH387 4.3 41.8 1.0 NE C:ARG164 4.5 25.1 1.0 N D:GLY109 4.5 24.2 1.0 H D:GLY109 4.6 29.1 1.0 HA3 C:GLY127 4.6 35.0 1.0 HD11 C:LEU125 4.8 29.6 1.0 O D:HOH356 4.8 14.4 1.0 HG2 C:GLN168 4.9 22.3 1.0

R.Abskharon, F.Wang, A.Wohlkonig, J.Ruan, S.Soror, G.Giachin, E.Pardon, W.Zou, G.Legname, J.Ma, J.Steyaert. Structural Evidence For the Critical Role of the Prion Protein Hydrophobic Region in Forming An Infectious Prion. Plos Pathog. V. 15 08139 2019.
ISSN: ESSN 1553-7374
PubMed: 31815959
DOI: 10.1371/JOURNAL.PPAT.1008139