Sodium in PDB 3ugx: Crystal Structure of Visual Arrestin

The structure of Crystal Structure of Visual Arrestin, PDB code: 3ugx was solved by R.Batra-Safferling, J.Granzin, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	32.89 / 2.65
Space group	P 21 21 2
Cell size a, b, c (Å), α, β, γ (°)	168.363, 184.329, 90.404, 90.00, 90.00, 90.00
R / Rfree (%)	20.9 / 25.3

The structure of Crystal Structure of Visual Arrestin also contains other interesting chemical elements:

Potassium

(K)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Visual Arrestin (pdb code 3ugx). 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 Visual Arrestin, PDB code: 3ugx:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Visual Arrestin


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 Visual Arrestin within 5.0Å range: probe atom residue distance (Å) B Occ A:Na413 b:34.3 occ:1.00 OG A:SER199 3.2 49.1 1.0 N A:GLU231 3.4 32.2 1.0 CB A:SER199 3.6 41.1 1.0 CB A:GLU231 3.7 24.5 1.0 O A:HOH471 3.8 47.1 1.0 CB A:THR230 3.8 39.4 1.0 CG A:GLU231 4.0 40.0 1.0 NZ A:LYS232 4.0 41.6 1.0 OE1 A:GLU231 4.0 36.9 1.0 CA A:THR230 4.0 32.7 1.0 CA A:GLU231 4.2 30.1 1.0 CD A:GLU231 4.2 55.4 1.0 C A:THR230 4.2 35.4 1.0 CD A:LYS232 4.2 42.5 1.0 CA A:SER199 4.4 30.0 1.0 OG1 A:THR230 4.6 29.8 1.0 O A:HOH417 4.6 38.4 1.0 N A:LYS232 4.7 36.4 1.0 CE A:LYS232 4.7 36.7 1.0 CG2 A:THR230 4.8 30.4 1.0 C A:GLU231 4.9 41.7 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Visual Arrestin


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 Visual Arrestin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na408 b:45.2 occ:1.00 O B:HOH426 2.3 47.4 1.0 O B:GLN195 2.8 31.0 1.0 O B:HOH411 2.8 33.5 1.0 O B:HOH431 3.0 40.8 1.0 CB B:GLN195 3.6 24.3 1.0 C B:GLN195 3.7 34.9 1.0 CB A:PRO269 3.8 28.2 1.0 N B:GLN195 3.9 43.5 1.0 O B:HOH423 3.9 37.5 1.0 CA B:GLN195 3.9 37.4 1.0 CE2 B:PHE197 4.0 43.4 1.0 CD2 B:PHE197 4.2 35.0 1.0 CG B:GLN195 4.5 43.8 1.0 CG A:PRO269 4.8 35.0 1.0 CA A:PRO269 4.8 34.6 1.0 N B:PHE196 5.0 34.4 1.0

J.Granzin, A.Cousin, M.Weirauch, R.Schlesinger, G.Buldt, R.Batra-Safferling. Crystal Structure of P44, A Constitutively Active Splice Variant of Visual Arrestin. J.Mol.Biol. V. 416 611 2012.
ISSN: ISSN 0022-2836
PubMed: 22306737
DOI: 10.1016/J.JMB.2012.01.028