Sodium in PDB 7zn3: Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the L State at pH 8.2 in the Presence of Sodium at 100K

The structure of Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the L State at pH 8.2 in the Presence of Sodium at 100K, PDB code: 7zn3 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)	19.98 / 1.60
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	68.39, 109.49, 119.39, 90, 90, 90
R / Rfree (%)	20.3 / 21.7

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the L State at pH 8.2 in the Presence of Sodium at 100K (pdb code 7zn3). 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 L State at pH 8.2 in the Presence of Sodium at 100K, PDB code: 7zn3:
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 L State at pH 8.2 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 L State at pH 8.2 in the Presence of Sodium at 100K within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:24.5 occ:1.00 OE2 A:GLU34 2.3 34.5 1.0 O A:ALA84 2.4 26.9 1.0 OE1 A:GLU34 2.4 34.7 1.0 OG1 A:THR88 2.4 23.2 1.0 OD2 A:ASP214 2.4 26.2 1.0 CD A:GLU34 2.6 34.2 1.0 C A:ALA84 3.3 22.5 1.0 CG A:ASP214 3.4 28.6 1.0 N A:THR88 3.6 19.5 1.0 CB A:THR88 3.6 26.1 1.0 OD1 A:ASP214 3.7 25.2 1.0 CA A:ALA84 3.7 25.4 1.0 CD1 A:LEU218 3.9 31.3 1.0 CA A:THR88 3.9 22.7 1.0 CB A:ALA84 4.0 22.7 1.0 CG A:GLU34 4.2 29.5 1.0 O A:HOH618 4.2 25.6 1.0 O A:HOH651 4.3 29.1 1.0 C A:LEU87 4.3 20.4 1.0 CB A:LEU87 4.3 24.8 1.0 N A:LEU85 4.4 22.9 1.0 O A:HOH605 4.6 36.9 1.0 CB A:ASP214 4.8 26.9 1.0 CA A:LEU87 4.8 23.5 1.0 CG2 A:THR88 4.8 23.4 1.0 CA A:LEU85 4.9 23.2 1.0 CB A:GLU34 4.9 24.6 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the L State at pH 8.2 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 L State at pH 8.2 in the Presence of Sodium at 100K within 5.0Å range: probe atom residue distance (Å) B Occ B:Na309 b:25.0 occ:1.00 OE2 B:GLU34 2.3 35.0 1.0 OG1 B:THR88 2.3 27.5 1.0 O B:ALA84 2.4 21.6 1.0 OE1 B:GLU34 2.4 31.5 1.0 OD2 B:ASP214 2.5 27.8 1.0 CD B:GLU34 2.7 35.1 1.0 C B:ALA84 3.3 20.7 1.0 CG B:ASP214 3.5 26.7 1.0 CB B:THR88 3.5 23.8 1.0 N B:THR88 3.6 24.9 1.0 CA B:ALA84 3.7 18.9 1.0 OD1 B:ASP214 3.7 28.9 1.0 CD1 B:LEU218 3.9 30.4 1.0 CA B:THR88 3.9 25.0 1.0 CB B:ALA84 4.0 24.1 1.0 O B:HOH412 4.1 28.8 1.0 CG B:GLU34 4.2 31.5 1.0 O B:HOH445 4.2 31.4 1.0 C B:LEU87 4.4 26.4 1.0 N B:LEU85 4.4 23.0 1.0 CB B:LEU87 4.4 20.4 1.0 O B:HOH401 4.5 46.7 1.0 CG2 B:THR88 4.7 24.7 1.0 CA B:LEU85 4.8 19.3 1.0 CB B:ASP214 4.8 24.6 1.0 CA B:LEU87 4.8 24.6 1.0 CB B:GLU34 4.9 26.0 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Light-Driven Inward Proton Pump Xenorhodopsin Bcxer in the L State at pH 8.2 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 L State at pH 8.2 in the Presence of Sodium at 100K within 5.0Å range: probe atom residue distance (Å) B Occ C:Na306 b:24.7 occ:1.00 OE2 C:GLU34 2.2 33.9 1.0 OE1 C:GLU34 2.4 30.1 1.0 OG1 C:THR88 2.4 23.6 1.0 OD2 C:ASP214 2.4 25.3 1.0 O C:ALA84 2.5 23.1 1.0 CD C:GLU34 2.6 39.0 1.0 C C:ALA84 3.3 21.3 1.0 CG C:ASP214 3.4 27.4 1.0 N C:THR88 3.6 21.5 1.0 CB C:THR88 3.6 23.3 1.0 OD1 C:ASP214 3.7 26.9 1.0 CA C:ALA84 3.7 22.8 1.0 CD1 C:LEU218 3.9 25.1 1.0 CA C:THR88 3.9 22.1 1.0 CB C:ALA84 4.0 22.1 1.0 CG C:GLU34 4.1 31.9 1.0 O C:HOH419 4.2 28.4 1.0 O C:HOH450 4.3 32.5 1.0 C C:LEU87 4.3 26.4 1.0 N C:LEU85 4.4 20.9 1.0 CB C:LEU87 4.5 24.2 1.0 O C:HOH408 4.7 36.7 1.0 CB C:ASP214 4.8 23.1 1.0 CG2 C:THR88 4.8 24.5 1.0 CA C:LEU87 4.8 23.8 1.0 CB C:GLU34 4.8 25.9 1.0 CA C:LEU85 4.9 23.8 1.0

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