Sodium in PDB 6s6c: Ground State Structure of Archaerhodopsin-3 at 100K

The structure of Ground State Structure of Archaerhodopsin-3 at 100K, PDB code: 6s6c was solved by I.Moraes, P.J.Judge, D.Axford, T.O.C.Kwan, 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)	52.10 / 1.07
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	44.669, 47.357, 104.193, 90.00, 90.00, 90.00
R / Rfree (%)	15.8 / 17

The structure of Ground State 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 Ground State Structure of Archaerhodopsin-3 at 100K (pdb code 6s6c). 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 Ground State Structure of Archaerhodopsin-3 at 100K, PDB code: 6s6c:

Sodium binding site 1 out of 1 in the Ground State 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 Ground State Structure of Archaerhodopsin-3 at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na714 b:18.4 occ:1.00 H A:LEU13 2.0 13.8 1.0 HG1 A:THR20 2.5 15.7 0.0 OD1 A:ASP11 2.6 12.9 1.0 OG1 A:THR20 2.7 12.1 1.0 HB2 A:LEU13 2.7 14.4 1.0 OD1 A:ASP15 2.7 13.4 1.0 N A:LEU13 2.9 13.6 1.0 HG22 A:THR20 3.0 12.1 1.0 HG23 A:THR20 3.1 12.2 1.0 HB2 A:ARG17 3.1 12.0 1.0 H A:ASP15 3.2 13.2 1.0 O A:ARG17 3.3 12.7 1.0 HA A:ASP11 3.3 12.3 1.0 H A:LEU12 3.3 13.2 1.0 H A:GLY14 3.4 13.3 1.0 CG2 A:THR20 3.4 12.2 1.0 H A:ARG17 3.4 11.8 1.0 N A:LEU12 3.5 13.0 1.0 CB A:LEU13 3.5 14.4 1.0 CB A:THR20 3.5 12.0 1.0 CA A:LEU13 3.6 13.7 1.0 HG A:LEU13 3.6 16.1 1.0 C A:ASP11 3.6 12.5 1.0 CG A:ASP15 3.7 13.7 1.0 CG A:ASP11 3.8 11.6 1.0 N A:GLY14 3.8 13.1 1.0 CA A:ASP11 3.9 12.3 1.0 HB A:THR20 3.9 12.1 1.0 HB2 A:LEU12 3.9 16.6 1.0 C A:LEU12 4.0 14.5 1.0 C A:LEU13 4.0 13.9 1.0 CB A:ARG17 4.0 12.1 1.0 HD11 A:LEU13 4.0 17.6 1.0 CG A:LEU13 4.0 16.1 1.0 C A:ARG17 4.1 11.8 1.0 N A:ASP15 4.1 13.1 1.0 OD2 A:ASP15 4.1 16.4 1.0 CA A:LEU12 4.2 14.9 1.0 O A:ASP11 4.2 13.5 1.0 N A:ARG17 4.2 11.6 1.0 HH21 A:ARG17 4.3 11.9 1.0 HB3 A:LEU13 4.3 14.6 1.0 HG21 A:THR20 4.3 12.3 1.0 HE A:ARG17 4.3 12.1 1.0 CA A:ARG17 4.3 11.8 1.0 H A:THR20 4.3 11.2 1.0 CB A:ASP11 4.4 12.0 1.0 HB3 A:ARG17 4.4 12.1 1.0 HA A:LEU13 4.5 13.8 1.0 CB A:LEU12 4.6 17.1 1.0 CD1 A:LEU13 4.6 17.9 1.0 NH2 A:ARG17 4.6 12.0 1.0 NE A:ARG17 4.6 12.4 1.0 H A:GLY16 4.7 12.4 1.0 CB A:ASP15 4.7 14.6 1.0 CA A:ASP15 4.8 13.0 1.0 OD2 A:ASP11 4.8 11.9 1.0 CA A:THR20 4.8 11.5 1.0 CZ A:ARG17 4.8 11.6 1.0 HB2 A:ASP11 4.9 11.9 1.0 HB3 A:LEU12 4.9 16.9 1.0 CA A:GLY14 4.9 13.8 1.0 HG3 A:ARG17 4.9 11.9 1.0 O A:LEU13 4.9 16.5 1.0 N A:GLY16 5.0 12.2 1.0 N A:THR20 5.0 11.2 1.0 C A:ASP15 5.0 12.6 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, T.O.C.Kwan, R.Reis, A.M.Orville, A.Watts, I.Moraes. Structure of the Archaerhodopsin-3 at 100K To Be Published.