Sodium in PDB 4ubz: Crystal Structure of A Prion Peptide

The structure of Crystal Structure of A Prion Peptide, PDB code: 4ubz was solved by L.Yu, S.-J.Lee, V.Yee, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	12.48 / 1.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	11.609, 18.107, 17.843, 90.00, 105.24, 90.00
R / Rfree (%)	8.8 / 11

The binding sites of Sodium atom in the Crystal Structure of A Prion Peptide (pdb code 4ubz). 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 Crystal Structure of A Prion Peptide, PDB code: 4ubz:

Sodium binding site 1 out of 1 in the Crystal Structure of A Prion Peptide


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of A Prion Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na201 b:3.3 occ:1.00 O A:HOH205 2.2 6.8 0.5 O A:HOH205 3.0 3.0 0.5 O A:HOH203 3.3 6.7 1.0 O B:GLY131 3.4 3.2 1.0 C B:GLY131 3.7 2.4 1.0 CE1 A:TYR128 3.7 2.5 1.0 O A:GLY126 3.7 2.4 1.0 CA A:GLY127 3.9 2.3 1.0 CA B:GLY131 4.0 1.9 1.0 CD1 A:TYR128 4.2 2.3 1.0 OXT B:GLY131 4.3 2.5 1.0 C A:GLY126 4.4 2.1 1.0 O B:HOH302 4.5 4.0 1.0 N A:GLY127 4.5 2.0 1.0 CZ A:TYR128 4.5 2.4 1.0 O A:HOH204 4.6 7.1 1.0 OH A:TYR128 4.8 2.8 1.0 C A:GLY127 4.8 1.9 1.0 O A:HOH202 4.9 6.8 1.0 O B:HOH301 4.9 6.0 1.0 N A:TYR128 4.9 1.6 1.0

L.Yu, S.J.Lee, V.C.Yee. Crystal Structures of Polymorphic Prion Protein Beta 1 Peptides Reveal Variable Steric Zipper Conformations. Biochemistry 2015.
ISSN: ISSN 0006-2960
PubMed: 25978088
DOI: 10.1021/ACS.BIOCHEM.5B00425