Sodium in PDB 6ivo: Crystal Structure of A Membrane Protein P208A

The structure of Crystal Structure of A Membrane Protein P208A, PDB code: 6ivo was solved by A.Kittredge, F.Fukuda, Y.Zhang, T.Yang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	48.76 / 2.45
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	114.009, 160.062, 161.843, 90.00, 90.00, 90.00
R / Rfree (%)	20.2 / 23.8

The structure of Crystal Structure of A Membrane Protein P208A also contains other interesting chemical elements:

Chlorine	(Cl)	12 atoms
Zinc	(Zn)	18 atoms

The binding sites of Sodium atom in the Crystal Structure of A Membrane Protein P208A (pdb code 6ivo). 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 A Membrane Protein P208A, PDB code: 6ivo:

Sodium binding site 1 out of 1 in the Crystal Structure of A Membrane Protein P208A


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 A Membrane Protein P208A within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:54.4 occ:1.00 OD2 C:ASP269 2.2 67.9 1.0 OD2 C:ASP261 2.4 83.3 1.0 O C:HOH438 2.6 63.7 1.0 O C:HOH432 2.8 49.6 1.0 CG C:ASP269 3.2 72.7 1.0 CG C:ASP261 3.4 77.3 1.0 CB C:ALA266 3.5 63.7 1.0 CA C:GLY264 3.6 64.1 1.0 OD1 C:ASP269 3.6 77.8 1.0 N C:ALA266 3.7 73.7 1.0 N C:THR265 3.8 73.3 1.0 CB C:ASP261 3.8 68.1 1.0 C C:GLY264 4.0 70.4 1.0 O C:ASP261 4.1 61.1 1.0 CA C:ALA266 4.3 69.9 1.0 OD1 C:ASP261 4.5 71.9 1.0 N C:GLY264 4.5 60.0 1.0 CB C:ASP269 4.6 63.8 1.0 C C:THR265 4.8 76.2 1.0 CA C:THR265 4.9 78.3 1.0 CA C:ASP261 5.0 64.1 1.0 C C:ASP261 5.0 61.0 1.0

C.Ji, A.Kittredge, A.Hopiavuori, N.Ward, S.Chen, Y.Fukuda, Y.Zhang, T.Yang. Dual CA2+-Dependent Gates in Human BESTROPHIN1 Underlie Disease-Causing Mechanisms of Gain-of-Function Mutations. Commun Biol V. 2 240 2019.
ISSN: ESSN 2399-3642
PubMed: 31263784
DOI: 10.1038/S42003-019-0433-3