Sodium in PDB 7zy3: Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation

The structure of Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation, PDB code: 7zy3 was solved by T.O.C.Kwan, P.J.Judge, I.Moraes, A.Watts, D.Axford, J.F.Bada Juarez, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.15 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	46.2, 48.3, 104.7, 90, 90, 90
R / Rfree (%)	16.5 / 18.2

The structure of Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation also contains other interesting chemical elements:

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

The binding sites of Sodium atom in the Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation (pdb code 7zy3). 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 Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation, PDB code: 7zy3:

Sodium binding site 1 out of 1 in the Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature Structure of Archaerhodopsin-3 Obtained 110 Ns After Photoexcitation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na714 b:34.6 occ:1.00 H A:LEU13 2.1 34.1 1.0 OD1 A:ASP11 2.6 26.4 1.0 OD1 A:ASP15 2.6 28.8 1.0 HB2 A:LEU13 2.7 36.3 1.0 OG1 A:THR20 2.7 28.7 1.0 HG22 A:THR20 2.8 30.1 1.0 N A:LEU13 2.9 28.4 1.0 HB2 A:ARG17 3.2 36.7 1.0 O A:ARG17 3.2 25.4 1.0 H A:ASP15 3.2 30.9 1.0 H A:LEU12 3.3 34.4 1.0 HA A:ASP11 3.3 35.5 1.0 CG2 A:THR20 3.4 25.1 1.0 HG1 A:THR20 3.4 34.4 1.0 H A:ARG17 3.4 31.4 1.0 HG23 A:THR20 3.4 30.1 1.0 H A:GLY14 3.4 38.5 1.0 N A:LEU12 3.5 28.7 1.0 CB A:LEU13 3.5 30.3 1.0 CB A:THR20 3.5 27.5 1.0 CA A:LEU13 3.6 28.6 1.0 CG A:ASP15 3.7 32.3 1.0 C A:ASP11 3.7 28.1 1.0 HG A:LEU13 3.7 53.7 1.0 CG A:ASP11 3.8 30.1 1.0 N A:GLY14 3.8 32.1 1.0 HB A:THR20 3.9 33.0 1.0 CA A:ASP11 3.9 29.5 1.0 C A:LEU12 4.0 33.0 1.0 HD11 A:LEU13 4.0 48.3 1.0 C A:LEU13 4.0 28.6 1.0 C A:ARG17 4.0 23.2 1.0 N A:ASP15 4.1 25.7 1.0 CB A:ARG17 4.1 30.6 1.0 N A:ARG17 4.1 26.1 1.0 CG A:LEU13 4.1 44.8 1.0 HB2 A:LEU12 4.2 41.4 1.0 CA A:LEU12 4.2 29.7 1.0 OD2 A:ASP15 4.2 32.8 1.0 HG21 A:THR20 4.3 30.1 1.0 HB3 A:LEU13 4.3 36.3 1.0 CA A:ARG17 4.3 25.0 1.0 O A:ASP11 4.3 28.6 1.0 HH21 A:ARG17 4.3 32.9 1.0 H A:THR20 4.4 29.1 1.0 HE A:ARG17 4.4 33.9 1.0 CB A:ASP11 4.4 27.4 1.0 HB3 A:ARG17 4.5 36.7 1.0 HA A:LEU13 4.5 34.3 1.0 CD1 A:LEU13 4.6 40.2 1.0 H A:GLY16 4.6 33.0 1.0 NH2 A:ARG17 4.7 27.4 1.0 CB A:LEU12 4.7 34.5 1.0 NE A:ARG17 4.7 28.2 1.0 OD2 A:ASP11 4.8 25.2 1.0 CB A:ASP15 4.8 27.4 1.0 CA A:ASP15 4.8 26.5 1.0 HB3 A:LEU12 4.8 41.4 1.0 N A:GLY16 4.8 27.5 1.0 CA A:GLY14 4.8 31.3 1.0 CA A:THR20 4.9 26.0 1.0 O A:LEU13 4.9 30.5 1.0 HB2 A:ASP11 4.9 32.9 1.0 CZ A:ARG17 4.9 29.7 1.0 C A:GLY14 4.9 31.3 1.0 C A:ASP15 4.9 29.3 1.0 HD13 A:LEU13 5.0 48.3 1.0

J.Birch, T.O.C.Kwan, P.J.Judge, D.Axford, J.F.Bada Juarez, P.Aller, A.Butryn, R.I.Reis, J.Vinals, E.Nango, R.Tanaka, K.Tono, Y.Joti, T.Tanaka, S.Owada, M.Sugahara, S.Iwata, R.L.Owen, A.M.Orville, A.Watts, I.Moraes. Vials: Versatile Approach to High-Density Microcrystals in Lipidic-Phase For Serial Crystallography To Be Published.