Sodium in PDB 3vhs: Crystal Structure of Ubz of Human WRNIP1

The structure of Crystal Structure of Ubz of Human WRNIP1, PDB code: 3vhs was solved by N.Suzuki, S.Wakatsuki, M.Kawasaki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.77 / 1.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	36.482, 73.457, 34.651, 90.00, 90.00, 90.00
R / Rfree (%)	21.3 / 26.2

The structure of Crystal Structure of Ubz of Human WRNIP1 also contains other interesting chemical elements:

Zinc

(Zn)

2 atoms

The binding sites of Sodium atom in the Crystal Structure of Ubz of Human WRNIP1 (pdb code 3vhs). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Ubz of Human WRNIP1, PDB code: 3vhs:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Ubz of Human WRNIP1


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 Ubz of Human WRNIP1 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na52 b:22.1 occ:0.50 O A:HOH72 1.8 38.1 1.0 O A:LEU40 2.3 46.1 1.0 O A:ASP37 2.3 37.3 1.0 C A:LEU40 3.5 45.7 1.0 C A:ASP37 3.5 36.7 1.0 OXT A:LEU40 4.0 46.8 1.0 CA A:ASP37 4.2 36.0 1.0 N A:ARG38 4.5 37.7 1.0 CA A:ARG38 4.7 39.9 1.0 CA A:LEU40 4.7 44.6 1.0 N A:LEU40 4.7 43.2 1.0 O A:ARG38 4.7 41.0 1.0 C A:ARG38 4.7 40.2 1.0 O A:LEU36 4.8 32.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Ubz of Human WRNIP1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Ubz of Human WRNIP1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na52 b:40.0 occ:1.00 O B:HOH62 1.9 27.5 0.5 O A:MET26 2.1 33.5 1.0 O B:HOH64 2.3 43.7 1.0 OD2 B:ASP37 2.5 46.4 1.0 O A:HOH69 2.5 36.0 1.0 OD1 B:ASP37 2.7 43.8 1.0 CG B:ASP37 3.0 41.8 1.0 C A:MET26 3.3 32.7 1.0 CA A:MET27 3.9 32.6 1.0 N A:MET27 4.0 32.3 1.0 CB A:MET27 4.3 31.8 1.0 CA A:MET26 4.4 32.8 1.0 O B:SER34 4.4 32.5 1.0 CB B:ASP37 4.5 40.5 1.0 OE1 A:GLN17 4.5 44.8 1.0 N A:MET26 4.5 32.2 1.0 CB A:MET26 4.7 33.2 1.0 NE2 A:GLN17 4.9 46.4 1.0

N.Suzuki, A.Rohaim, R.Kato, I.Dikic, S.Wakatsuki, M.Kawasaki. A Novel Mode of Ubiquitin Recognition By the Ubiquitin-Binding Zinc Finger Domain of WRNIP1. Febs J. 2016.
ISSN: ISSN 1742-464X
PubMed: 27062441
DOI: 10.1111/FEBS.13734