Sodium in PDB 2znd: Crystal Structure of CA2+-Free Form of DES3-20ALG-2

The structure of Crystal Structure of CA2+-Free Form of DES3-20ALG-2, PDB code: 2znd 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)	43.11 / 1.70
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	71.148, 48.833, 54.183, 90.00, 90.00, 90.00
R / Rfree (%)	19.3 / 22.2

The binding sites of Sodium atom in the Crystal Structure of CA2+-Free Form of DES3-20ALG-2 (pdb code 2znd). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of CA2+-Free Form of DES3-20ALG-2, PDB code: 2znd:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of CA2+-Free Form of DES3-20ALG-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 CA2+-Free Form of DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na194 b:15.2 occ:1.00 O A:VAL42 2.2 15.2 1.0 OD2 A:ASP38 2.3 15.1 1.0 OD1 A:ASP36 2.3 15.2 1.0 OE1 A:GLU47 2.3 14.8 1.0 O A:HOH268 2.6 22.9 1.0 OE2 A:GLU47 2.8 15.8 1.0 CD A:GLU47 2.9 16.5 1.0 CG A:ASP38 3.2 16.6 1.0 OG A:SER40 3.3 17.1 1.0 C A:VAL42 3.4 15.9 1.0 CG A:ASP36 3.5 14.3 1.0 OD1 A:ASP38 3.7 19.4 1.0 O A:HOH311 4.0 37.2 1.0 CA A:ILE43 4.0 14.0 1.0 CA A:ASP36 4.1 14.4 1.0 N A:ASP38 4.1 14.5 1.0 N A:ILE43 4.1 13.7 1.0 CB A:ASP36 4.3 14.2 1.0 C A:ASP36 4.3 15.0 1.0 N A:VAL42 4.3 16.4 1.0 CB A:ASP38 4.3 15.1 1.0 N A:SER44 4.4 13.2 1.0 CG A:GLU47 4.4 13.9 1.0 OD2 A:ASP36 4.4 15.9 1.0 N A:LYS37 4.4 14.0 1.0 CB A:SER40 4.4 15.7 1.0 N A:SER40 4.4 15.6 1.0 CA A:VAL42 4.5 15.7 1.0 N A:ARG39 4.5 14.9 1.0 CA A:ASP38 4.5 15.2 1.0 C A:ILE43 4.7 13.8 1.0 C A:ASP38 4.8 15.2 1.0 O A:ASP36 4.8 14.5 1.0 CA A:SER40 4.9 16.1 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of CA2+-Free Form of DES3-20ALG-2


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 CA2+-Free Form of DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na195 b:17.2 occ:1.00 O A:HOH221 2.3 18.9 1.0 O A:MET109 2.4 13.1 1.0 OD1 A:ASP105 2.4 17.6 1.0 OD1 A:ASP103 2.4 13.1 1.0 OG A:SER107 2.5 16.7 1.0 CG A:ASP103 3.5 11.6 1.0 CB A:SER107 3.5 15.4 1.0 CG A:ASP105 3.5 18.3 1.0 C A:MET109 3.6 12.9 1.0 O A:HOH240 3.7 21.6 1.0 OE1 A:GLU114 3.7 15.7 1.0 O A:HOH251 3.8 29.0 1.0 N A:SER107 3.9 14.2 1.0 OD2 A:ASP105 4.0 22.6 1.0 O A:HOH294 4.0 28.5 1.0 CA A:ASP103 4.2 12.0 1.0 OD2 A:ASP103 4.2 12.8 1.0 N A:MET109 4.3 13.7 1.0 CA A:SER107 4.3 15.0 1.0 CB A:ASP103 4.3 12.1 1.0 OE1 A:GLN145 4.3 21.2 1.0 OE2 A:GLU114 4.3 15.4 1.0 C A:ASP103 4.3 12.4 1.0 N A:ASP105 4.4 14.2 1.0 CA A:ILE110 4.4 13.6 1.0 N A:ARG104 4.4 13.1 1.0 CD A:GLU114 4.5 14.8 1.0 N A:ILE110 4.5 12.7 1.0 CA A:MET109 4.5 13.5 1.0 N A:ASN106 4.7 13.7 1.0 CB A:ASP105 4.7 15.7 1.0 N A:GLY108 4.8 14.0 1.0 CA A:ASP105 4.9 14.5 1.0 C A:SER107 4.9 15.3 1.0 O A:ASP103 4.9 13.1 1.0 C A:ASP105 4.9 14.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of CA2+-Free Form of DES3-20ALG-2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of CA2+-Free Form of DES3-20ALG-2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na196 b:17.1 occ:1.00 OD1 A:ASP173 2.3 21.5 1.0 O A:TRP175 2.3 15.1 1.0 OD2 A:ASP171 2.3 19.6 1.0 OD1 A:ASP169 2.4 17.1 1.0 O A:HOH223 2.5 19.9 1.0 O A:HOH252 2.6 29.4 1.0 CG A:ASP173 3.3 25.1 1.0 C A:TRP175 3.4 15.9 1.0 CG A:ASP169 3.5 14.2 1.0 CG A:ASP171 3.5 23.1 1.0 OD2 A:ASP173 3.8 25.4 1.0 CA A:ASP169 4.0 14.9 1.0 N A:TRP175 4.0 17.3 1.0 N A:ASP173 4.0 22.0 1.0 OD1 A:ASP171 4.1 24.7 1.0 N A:ASP171 4.1 20.5 1.0 CA A:TRP175 4.1 16.9 1.0 N A:THR170 4.2 17.6 1.0 C A:ASP169 4.2 16.1 1.0 CB A:ASP169 4.3 14.7 1.0 OD2 A:ASP169 4.3 16.2 1.0 CB A:TRP175 4.4 18.0 1.0 CB A:ASP173 4.4 22.8 1.0 N A:ILE176 4.4 14.6 1.0 N A:GLN172 4.5 22.1 1.0 CA A:ILE176 4.6 14.6 1.0 CA A:ASP173 4.6 22.7 1.0 CB A:ASP171 4.7 21.5 1.0 CA A:ASP171 4.7 21.8 1.0 C A:ASP171 4.7 22.1 1.0 O A:HOH206 4.7 18.6 1.0 N A:GLY174 4.7 20.5 1.0 C A:ASP173 4.9 21.6 1.0 O A:ASP169 4.9 16.5 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