Sodium in PDB 6gux: Dark-Adapted Structure of Archaerhodopsin-3 at 100K

The structure of Dark-Adapted Structure of Archaerhodopsin-3 at 100K, PDB code: 6gux was solved by I.Moraes, P.J.Judge, J.F.Bada Juarez, J.Vinals, D.Axford, A.Watts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.29 / 1.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.701, 47.525, 104.421, 90.00, 90.00, 90.00
R / Rfree (%)	14 / 17.2

The structure of Dark-Adapted Structure of Archaerhodopsin-3 at 100K also contains other interesting chemical elements:

Calcium	(Ca)	1 atom
Chlorine	(Cl)	3 atoms

The binding sites of Sodium atom in the Dark-Adapted Structure of Archaerhodopsin-3 at 100K (pdb code 6gux). 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 Dark-Adapted Structure of Archaerhodopsin-3 at 100K, PDB code: 6gux:

Sodium binding site 1 out of 1 in the Dark-Adapted Structure of Archaerhodopsin-3 at 100K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Dark-Adapted Structure of Archaerhodopsin-3 at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na714 b:17.9 occ:1.00 H A:LEU13 2.0 13.4 1.0 HG1 A:THR20 2.0 11.2 0.0 OD1 A:ASP11 2.6 12.4 1.0 HB2 A:LEU13 2.7 14.4 1.0 OG1 A:THR20 2.7 11.4 1.0 OD1 A:ASP15 2.8 13.9 1.0 N A:LEU13 2.9 13.2 1.0 HG22 A:THR20 3.1 10.7 1.0 HG23 A:THR20 3.1 10.8 1.0 HB2 A:ARG17 3.2 10.5 1.0 H A:ASP15 3.2 12.3 1.0 O A:ARG17 3.3 11.1 1.0 HA A:ASP11 3.3 11.5 1.0 H A:LEU12 3.3 12.4 1.0 H A:GLY14 3.4 12.5 1.0 CG2 A:THR20 3.4 10.8 1.0 CB A:LEU13 3.4 14.3 1.0 H A:ARG17 3.4 11.1 1.0 N A:LEU12 3.4 12.1 1.0 CB A:THR20 3.5 10.0 1.0 CA A:LEU13 3.5 13.3 1.0 HG A:LEU13 3.6 16.5 1.0 C A:ASP11 3.6 11.4 1.0 CG A:ASP15 3.7 14.6 1.0 CG A:ASP11 3.8 11.2 1.0 N A:GLY14 3.8 12.3 1.0 CA A:ASP11 3.9 11.6 1.0 HB A:THR20 3.9 10.2 1.0 C A:LEU13 3.9 13.4 1.0 C A:LEU12 3.9 14.7 1.0 HB2 A:LEU12 3.9 16.4 1.0 HD11 A:LEU13 4.0 18.0 1.0 CG A:LEU13 4.0 16.3 1.0 CB A:ARG17 4.1 10.3 1.0 C A:ARG17 4.1 10.3 1.0 N A:ASP15 4.1 12.0 1.0 CA A:LEU12 4.1 14.2 1.0 O A:ASP11 4.2 12.3 1.0 OD2 A:ASP15 4.2 17.6 1.0 N A:ARG17 4.2 10.9 1.0 HB3 A:LEU13 4.2 14.4 1.0 HG21 A:THR20 4.3 10.6 1.0 CA A:ARG17 4.3 10.7 1.0 H A:THR20 4.3 9.7 1.0 HH21 A:ARG17 4.4 11.3 1.0 CB A:ASP11 4.4 11.5 1.0 HE A:ARG17 4.4 11.3 1.0 HA A:LEU13 4.4 13.2 1.0 HB3 A:ARG17 4.5 10.4 1.0 CD1 A:LEU13 4.5 18.3 1.0 CB A:LEU12 4.6 17.1 1.0 NH2 A:ARG17 4.7 11.5 1.0 NE A:ARG17 4.8 11.6 1.0 CB A:ASP15 4.8 14.3 1.0 H A:GLY16 4.8 11.7 1.0 OD2 A:ASP11 4.8 10.4 1.0 CA A:THR20 4.8 9.7 1.0 CA A:ASP15 4.8 12.4 1.0 HB2 A:ASP11 4.8 11.3 1.0 O A:LEU13 4.9 16.2 1.0 CA A:GLY14 4.9 12.8 1.0 HB3 A:LEU12 4.9 16.8 1.0 CZ A:ARG17 4.9 10.9 1.0 HG3 A:ARG17 5.0 11.0 1.0 N A:GLY16 5.0 11.6 1.0 C A:ASP15 5.0 12.6 1.0 N A:THR20 5.0 9.7 1.0

J.F.Bada Juarez, P.J.Judge, J.Vinals, D.Axford, J.Birch, P.Aller, A.Butryn, R.L.Owen, D.A.Sherrell, J.H.Beale, A.M.Orville, A.Watts, I.Moraes. Structure of the Archaerhodopsin-3 at 100K To Be Published.