Sodium in PDB 6s63: Dark-Adapted Structure of Archaerhodopsin-3 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature

The structure of Dark-Adapted Structure of Archaerhodopsin-3 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature, PDB code: 6s63 was solved by I.Moraes, P.J.Judge, D.Axford, J.F.Bada Juarez, J.Vinals, A.Watts, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	52.68 / 1.85
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	45.910, 48.351, 105.364, 90.00, 90.00, 90.00
R / Rfree (%)	17.5 / 19.2

The structure of Dark-Adapted Structure of Archaerhodopsin-3 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature 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 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature (pdb code 6s63). 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 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature, PDB code: 6s63:

Sodium binding site 1 out of 1 in the Dark-Adapted Structure of Archaerhodopsin-3 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature


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 Obtained From Lcp Crystals Using A Thin-Film Sandwich at Room Temperature within 5.0Å range: probe atom residue distance (Å) B Occ A:Na714 b:21.7 occ:1.00 H A:LEU13 2.2 23.7 1.0 OD1 A:ASP11 2.5 17.6 1.0 OD1 A:ASP15 2.6 18.7 1.0 OG1 A:THR20 2.7 16.2 1.0 HB2 A:LEU13 2.8 26.6 1.0 HB2 A:ARG17 3.1 20.2 1.0 N A:LEU13 3.1 19.7 1.0 HG21 A:THR20 3.1 18.4 1.0 H A:ASP15 3.1 21.9 1.0 O A:ARG17 3.1 16.4 1.0 HG23 A:THR20 3.2 18.4 1.0 H A:ARG17 3.2 21.6 1.0 HA A:ASP11 3.3 20.9 1.0 HG1 A:THR20 3.3 19.6 1.0 H A:GLY14 3.3 22.7 1.0 H A:LEU12 3.3 21.9 1.0 CG2 A:THR20 3.4 15.2 1.0 N A:LEU12 3.5 18.1 1.0 CB A:LEU13 3.6 22.1 1.0 CB A:THR20 3.6 15.1 1.0 CG A:ASP11 3.7 18.4 1.0 CG A:ASP15 3.7 18.8 1.0 C A:ASP11 3.7 20.3 1.0 CA A:LEU13 3.7 19.9 1.0 HG A:LEU13 3.7 28.9 1.0 N A:GLY14 3.8 18.8 1.0 CA A:ASP11 3.9 17.3 1.0 CB A:ARG17 3.9 16.7 1.0 C A:ARG17 3.9 16.4 1.0 N A:ARG17 4.0 17.8 1.0 HB A:THR20 4.0 18.2 1.0 C A:LEU13 4.0 18.9 1.0 C A:LEU12 4.1 19.7 1.0 N A:ASP15 4.1 18.1 1.0 HB2 A:LEU12 4.1 25.0 1.0 CA A:ARG17 4.2 17.4 1.0 CG A:LEU13 4.2 24.0 1.0 HD12 A:LEU13 4.2 31.5 1.0 OD2 A:ASP15 4.2 21.0 1.0 CA A:LEU12 4.2 19.6 1.0 HB3 A:ARG17 4.3 20.2 1.0 O A:ASP11 4.3 18.9 1.0 H A:THR20 4.3 17.1 1.0 CB A:ASP11 4.3 17.3 1.0 HH21 A:ARG17 4.3 23.2 1.0 HB3 A:LEU13 4.4 26.6 1.0 HE A:ARG17 4.4 18.8 1.0 HG22 A:THR20 4.4 18.4 1.0 H A:GLY16 4.5 20.6 1.0 HA A:LEU13 4.6 24.1 1.0 CB A:LEU12 4.6 20.7 1.0 OD2 A:ASP11 4.7 16.5 1.0 NH2 A:ARG17 4.7 19.2 1.0 CD1 A:LEU13 4.7 26.1 1.0 NE A:ARG17 4.7 15.5 1.0 CB A:ASP15 4.8 17.8 1.0 HB2 A:ASP11 4.8 20.9 1.0 N A:GLY16 4.8 17.0 1.0 HB3 A:LEU12 4.8 25.0 1.0 CA A:ASP15 4.8 17.6 1.0 CA A:GLY14 4.8 18.0 1.0 CA A:THR20 4.9 15.1 1.0 C A:ASP15 4.9 17.5 1.0 CZ A:ARG17 5.0 16.5 1.0 N A:THR20 5.0 14.2 1.0 O A:LEU13 5.0 20.1 1.0 HG3 A:ARG17 5.0 21.0 1.0 C A:GLY14 5.0 18.2 1.0

J.F.Bada Juarez, P.J.Judge, J.Vinals, D.Axford, J.Birch, P.Aller, A.Butryn, D.A.Sherrell, J.H.Beale, A.M.Orville, A.Watts, I.Moraes. Structure of Archaerhodopsin-3 Obtained From Lcp Crystals To Be Published.