Sodium in PDB 6yby: Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 4.6

The structure of Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 4.6, PDB code: 6yby was solved by K.Kovalev, I.Gushchin, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	19.83 / 1.80
Space group	I 2 2 2
Cell size a, b, c (Å), α, β, γ (°)	40.887, 83.601, 233.830, 90.00, 90.00, 90.00
R / Rfree (%)	20.1 / 22

The binding sites of Sodium atom in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 4.6 (pdb code 6yby). 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 Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 4.6, PDB code: 6yby:

Sodium binding site 1 out of 1 in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 4.6


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 D116N Mutant of the Light-Driven Sodium Pump KR2 in the Monomeric Form, pH 4.6 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:55.1 occ:1.00 O A:THR83 2.2 52.2 1.0 O A:HOH502 2.3 60.1 1.0 O A:PHE86 2.3 45.3 1.0 O A:HOH490 2.4 63.2 1.0 O A:HOH518 2.4 62.2 1.0 OH A:TYR25 2.6 51.0 1.0 C A:THR83 3.4 48.6 1.0 C A:PHE86 3.6 50.1 1.0 CZ A:TYR25 3.6 44.7 1.0 O A:HOH430 3.9 66.3 1.0 CA A:THR83 4.0 52.9 1.0 CE1 A:TYR25 4.0 42.6 1.0 O A:HOH522 4.2 74.3 1.0 CA A:THR87 4.2 50.5 0.5 CA A:THR87 4.3 53.8 0.5 O A:HOH479 4.3 51.5 1.0 N A:THR87 4.3 48.8 1.0 OG1 A:THR87 4.4 59.8 0.5 N A:SER84 4.5 42.3 1.0 O A:HOH468 4.5 56.9 1.0 CB A:THR83 4.6 50.4 1.0 N A:PHE86 4.6 42.7 1.0 CE2 A:TYR25 4.6 45.5 1.0 CA A:PHE86 4.6 46.8 1.0 CA A:SER84 4.8 48.9 0.5 CA A:SER84 4.8 50.0 0.5 CB A:THR87 4.8 49.0 0.5 CE2 A:TYR95 4.8 47.9 1.0 CD2 A:TYR95 4.9 51.5 1.0 CB A:THR87 4.9 56.0 0.5 C A:SER84 5.0 47.0 1.0

K.Kovalev, R.Astashkin, I.Gushchin, V.Gordeliy. Molecular Mechanism of Light-Driven Sodium Pumping To Be Published.