Sodium in PDB 7zna: Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K

The structure of Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K, PDB code: 7zna was solved by K.Kovalev, F.Tsybrov, A.Alekseev, G.Bourenkov, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.57, 109.59, 119.62, 90, 90, 90
R / Rfree (%)	19.7 / 23

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K (pdb code 7zna). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K, PDB code: 7zna:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K


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 the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1025 b:29.0 occ:0.50 O A:HOH1113 1.6 34.2 0.5 OE2 A:GLU34 1.9 44.2 0.5 O A:ALA84 2.3 23.0 1.0 OG1 A:THR88 2.4 22.6 1.0 OD2 A:ASP214 2.6 27.1 1.0 CD A:GLU34 2.8 43.1 0.5 OE2 A:GLU34 2.9 24.6 0.5 OE1 A:GLU34 3.2 43.9 0.5 C A:ALA84 3.2 21.6 1.0 CG A:ASP214 3.5 27.0 1.0 N A:THR88 3.6 22.6 1.0 CA A:ALA84 3.6 21.9 1.0 CB A:THR88 3.7 22.7 1.0 OD1 A:ASP214 3.7 24.8 1.0 CD1 A:LEU218 3.9 30.2 1.0 O A:HOH1115 3.9 25.3 1.0 CA A:THR88 3.9 22.8 1.0 CB A:ALA84 3.9 21.8 1.0 CD A:GLU34 4.0 23.6 0.5 CG A:GLU34 4.2 37.2 0.5 C A:LEU87 4.3 22.5 1.0 N A:LEU85 4.3 24.1 1.0 CB A:LEU87 4.3 22.9 1.0 CG A:GLU34 4.5 22.9 0.5 O A:HOH1153 4.6 27.0 1.0 CB A:GLU34 4.8 23.4 0.5 CG2 A:THR88 4.8 21.5 1.0 CA A:LEU87 4.8 23.2 1.0 CB A:GLU34 4.8 33.0 0.5 CB A:ASP214 4.9 22.4 1.0 CA A:LEU85 4.9 22.9 1.0 N A:ALA84 5.0 19.9 1.0 OE1 A:GLU34 5.0 17.9 0.5

Sodium binding site 2 out of 3 in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K within 5.0Å range: probe atom residue distance (Å) B Occ B:Na323 b:21.7 occ:0.30 O B:HOH425 1.6 36.2 0.7 OE2 B:GLU34 1.9 26.0 0.3 O B:ALA84 2.3 24.9 1.0 OG1 B:THR88 2.4 25.6 1.0 CD B:GLU34 2.5 25.4 0.3 OE1 B:GLU34 2.5 24.0 0.3 OE2 B:GLU34 2.6 31.5 0.7 OD2 B:ASP214 2.9 25.6 1.0 C B:ALA84 3.2 21.7 1.0 N B:THR88 3.3 23.8 1.0 CB B:THR88 3.6 23.9 1.0 CA B:ALA84 3.6 23.1 1.0 CD B:GLU34 3.7 31.7 0.7 CA B:THR88 3.7 22.6 1.0 CG B:ASP214 3.8 23.2 1.0 CD1 B:LEU218 3.8 28.8 1.0 OD1 B:ASP214 3.9 26.3 1.0 CG B:GLU34 4.0 24.9 0.3 O B:HOH415 4.0 23.4 1.0 C B:LEU87 4.0 24.8 1.0 CB B:LEU87 4.1 20.6 1.0 CB B:ALA84 4.1 22.5 1.0 CG B:GLU34 4.2 28.1 0.7 N B:LEU85 4.4 23.5 1.0 CA B:LEU87 4.5 21.9 1.0 O B:HOH423 4.6 28.7 1.0 CB B:GLU34 4.6 25.1 0.7 CB B:GLU34 4.7 24.0 0.3 OE1 B:GLU34 4.7 28.4 0.7 CG2 B:THR88 4.8 25.2 1.0 O B:LEU87 4.8 25.4 1.0 N B:LEU87 4.8 19.8 1.0 CA B:LEU85 4.9 21.8 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the Ground State at pH 5.2 in the Presence of Sodium at 100K within 5.0Å range: probe atom residue distance (Å) B Occ C:Na723 b:25.6 occ:0.50 O C:HOH806 1.7 27.7 0.5 OE2 C:GLU34 1.9 36.6 0.5 O C:ALA84 2.4 22.6 1.0 OG1 C:THR88 2.4 23.5 1.0 CD C:GLU34 2.6 37.6 0.5 OE1 C:GLU34 2.7 33.5 0.5 OE2 C:GLU34 2.7 33.9 0.5 OD2 C:ASP214 2.7 29.7 1.0 C C:ALA84 3.3 21.5 1.0 CG C:ASP214 3.6 30.7 1.0 N C:THR88 3.6 23.5 1.0 CB C:THR88 3.7 27.9 1.0 CA C:ALA84 3.7 22.6 1.0 CD C:GLU34 3.7 29.6 0.5 OD1 C:ASP214 3.8 29.2 1.0 CD1 C:LEU218 3.8 30.0 1.0 O C:HOH823 3.9 25.8 1.0 CA C:THR88 3.9 27.2 1.0 CB C:ALA84 4.0 24.4 1.0 CG C:GLU34 4.1 34.9 0.5 CG C:GLU34 4.2 29.2 0.5 C C:LEU87 4.3 25.8 1.0 CB C:LEU87 4.3 23.4 1.0 O C:HOH858 4.4 31.6 1.0 N C:LEU85 4.4 22.8 1.0 CB C:GLU34 4.6 26.7 0.5 CB C:GLU34 4.7 31.1 0.5 OE1 C:GLU34 4.8 24.6 0.5 CA C:LEU87 4.8 23.2 1.0 CG2 C:THR88 4.8 28.7 1.0 CB C:ASP214 5.0 27.6 1.0

K.Kovalev, F.Tsybrov, A.Alekseev, V.Gordeliy. Molecular Mechanism of Inward Proton Translocation To Be Published.