Sodium in PDB 2zn8: Crystal Structure of ZN2+-Bound Form of Alg-2

The structure of Crystal Structure of ZN2+-Bound Form of Alg-2, PDB code: 2zn8 was solved by H.Suzuki, M.Kawasaki, T.Inuzuka, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.10 / 2.70
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	72.010, 169.738, 46.343, 90.00, 90.00, 90.00
R / Rfree (%)	21.1 / 26

The structure of Crystal Structure of ZN2+-Bound Form of Alg-2 also contains other interesting chemical elements:

Zinc

(Zn)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of ZN2+-Bound Form of Alg-2 (pdb code 2zn8). 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 ZN2+-Bound Form of Alg-2, PDB code: 2zn8:

Sodium binding site 1 out of 1 in the Crystal Structure of ZN2+-Bound Form of Alg-2


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 ZN2+-Bound Form of Alg-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na995 b:25.9 occ:1.00 O A:TRP175 2.4 26.8 1.0 OD1 A:ASP171 2.5 34.3 1.0 OD1 A:ASP169 2.6 34.7 1.0 OD1 A:ASP173 2.7 29.6 1.0 ZN A:ZN993 3.0 28.0 1.0 C A:TRP175 3.4 26.6 1.0 CG A:ASP171 3.4 33.6 1.0 CG A:ASP173 3.5 30.2 1.0 CG A:ASP169 3.7 35.4 1.0 OD2 A:ASP173 3.8 27.4 1.0 OD2 A:ASP171 3.8 32.8 1.0 N A:TRP175 4.0 27.8 1.0 CA A:TRP175 4.0 27.0 1.0 CB A:TRP175 4.1 26.4 1.0 CA A:ASP169 4.2 35.5 1.0 N A:ILE176 4.3 26.2 1.0 N A:ASP171 4.4 35.1 1.0 CB A:ASP169 4.4 35.5 1.0 N A:ASP173 4.4 32.9 1.0 C A:ASP169 4.5 35.5 1.0 N A:THR170 4.6 35.5 1.0 CA A:ILE176 4.6 25.9 1.0 OD2 A:ASP169 4.7 33.8 1.0 N A:GLN172 4.7 35.1 1.0 CB A:ASP171 4.7 34.4 1.0 CB A:ASP173 4.8 31.2 1.0 CA A:ASP171 4.9 34.7 1.0 C A:ASP171 4.9 34.9 1.0 CA A:ASP173 5.0 31.3 1.0

H.Suzuki, M.Kawasaki, T.Inuzuka, M.Okumura, T.Kakiuchi, H.Shibata, S.Wakatsuki, M.Maki. Structural Basis For Ca(2+)-Dependent Formation of Alg-2/Alix Peptide Complex: Ca(2+)/EF3-Driven Arginine Switch Mechanism Structure V. 16 1562 2008.
ISSN: ISSN 0969-2126
PubMed: 18940611
DOI: 10.1016/J.STR.2008.07.012