Sodium in PDB 2zne: Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide

The structure of Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide, PDB code: 2zne 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)	33.94 / 2.20
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	47.449, 88.509, 211.556, 90.00, 90.00, 90.00
R / Rfree (%)	22.3 / 27.4

The structure of Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide also contains other interesting chemical elements:

Zinc

(Zn)

8 atoms

The binding sites of Sodium atom in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide (pdb code 2zne). 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 ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide, PDB code: 2zne:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs 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 ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range: probe atom residue distance (Å) B Occ A:Na995 b:33.0 occ:1.00 O A:HOH1019 2.2 25.8 1.0 O A:TRP175 2.3 28.2 1.0 OD1 A:ASP173 2.3 37.8 1.0 OD1 A:ASP169 2.5 35.2 1.0 OD2 A:ASP171 2.5 47.0 1.0 O A:HOH1000 3.2 34.5 1.0 ZN A:ZN993 3.4 49.8 1.0 C A:TRP175 3.4 28.2 1.0 CG A:ASP173 3.4 39.3 1.0 CG A:ASP171 3.4 46.6 1.0 CG A:ASP169 3.6 37.9 1.0 OD1 A:ASP171 3.7 44.3 1.0 OD2 A:ASP173 3.8 39.5 1.0 CA A:ASP169 3.9 41.0 1.0 N A:TRP175 3.9 28.6 1.0 CA A:TRP175 4.1 28.1 1.0 N A:THR170 4.1 44.0 1.0 CB A:TRP175 4.2 28.2 1.0 C A:ASP169 4.3 42.7 1.0 CB A:ASP169 4.3 39.5 1.0 N A:ASP173 4.3 40.3 1.0 N A:ASP171 4.3 45.6 1.0 N A:ILE176 4.4 28.2 1.0 OD2 A:ASP169 4.5 34.3 1.0 CA A:ILE176 4.6 27.9 1.0 CB A:ASP173 4.7 38.8 1.0 N A:GLY174 4.7 34.8 1.0 N A:GLN172 4.7 44.9 1.0 CB A:ASP171 4.8 45.8 1.0 O A:TYR168 4.9 41.2 1.0 CA A:ASP173 4.9 38.3 1.0 CA A:ASP171 5.0 45.9 1.0 C A:ASP173 5.0 37.1 1.0 C A:ASP171 5.0 45.6 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide


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 ZN2+-Bound Form of DES3-23ALG-2 Complexed with Alix Abs Peptide within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1 b:26.7 occ:1.00 O B:HOH1005 2.2 21.9 1.0 OD1 B:ASP171 2.3 38.7 1.0 OD2 B:ASP173 2.4 30.8 1.0 O B:TRP175 2.4 22.6 1.0 OD1 B:ASP169 2.4 29.8 1.0 O B:HOH1017 2.6 34.4 1.0 CG B:ASP171 3.3 34.9 1.0 ZN B:ZN993 3.4 37.3 1.0 CG B:ASP173 3.4 32.4 1.0 C B:TRP175 3.4 24.0 1.0 CG B:ASP169 3.5 29.4 1.0 OD2 B:ASP171 3.7 30.8 1.0 OD1 B:ASP173 3.9 33.6 1.0 N B:TRP175 4.0 25.3 1.0 CA B:ASP169 4.0 31.5 1.0 CA B:TRP175 4.1 24.5 1.0 N B:ASP173 4.2 31.3 1.0 CB B:TRP175 4.2 24.6 1.0 C B:ASP169 4.3 32.6 1.0 N B:ASP171 4.3 34.8 1.0 CB B:ASP169 4.3 30.3 1.0 OD2 B:ASP169 4.4 29.3 1.0 N B:GLN172 4.4 33.9 1.0 N B:THR170 4.5 33.9 1.0 N B:ILE176 4.5 24.4 1.0 O B:HOH1016 4.5 24.2 1.0 CB B:ASP171 4.6 34.1 1.0 C B:ASP171 4.6 34.0 1.0 CB B:ASP173 4.6 31.2 1.0 CA B:ILE176 4.7 24.6 1.0 CA B:ASP171 4.7 34.2 1.0 N B:GLY174 4.7 28.8 1.0 CA B:ASP173 4.8 30.9 1.0 O B:ASP169 4.8 32.5 1.0 C B:ASP173 4.9 30.0 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