Sodium in PDB 6ybz: Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0

The structure of Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6ybz 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)	20.00 / 2.35
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.343, 240.477, 135.415, 90.00, 90.00, 90.00
R / Rfree (%)	19.6 / 21.8

The binding sites of Sodium atom in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 (pdb code 6ybz). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6ybz:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


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 Pentameric Form, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:31.6 occ:1.00 O A:THR83 2.2 24.0 1.0 O A:HOH433 2.3 29.8 1.0 O A:PHE86 2.3 26.7 1.0 OH A:TYR25 2.5 26.4 1.0 OD1 B:ASP102 2.6 34.3 1.0 C A:THR83 3.3 19.9 1.0 CG B:ASP102 3.3 39.1 1.0 OD2 B:ASP102 3.4 39.8 1.0 CZ A:TYR25 3.5 22.9 1.0 C A:PHE86 3.5 26.2 1.0 O B:HOH412 3.8 24.3 1.0 CA A:THR83 3.9 19.9 1.0 CE1 A:TYR25 3.9 21.9 1.0 CA A:THR87 4.3 28.8 1.0 N A:THR87 4.3 27.9 1.0 CB A:THR83 4.3 18.1 1.0 CE2 A:TYR25 4.4 20.0 1.0 N A:SER84 4.5 21.5 0.5 N A:SER84 4.5 20.3 0.5 OG1 A:THR87 4.6 36.8 1.0 CA A:PHE86 4.6 25.7 1.0 N A:PHE86 4.6 25.6 1.0 CB B:ASP102 4.8 34.2 1.0 CD2 A:TYR95 4.9 22.6 1.0 CA A:SER84 4.9 22.5 0.5 CA A:SER84 4.9 20.4 0.5

Sodium binding site 2 out of 5 in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


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 D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:30.1 occ:1.00 O B:THR83 2.2 27.3 1.0 O B:PHE86 2.3 29.6 1.0 O B:HOH427 2.4 47.4 1.0 OH B:TYR25 2.5 23.8 1.0 OD1 C:ASP102 2.6 35.6 1.0 C B:THR83 3.3 21.6 1.0 CG C:ASP102 3.3 41.5 1.0 OD2 C:ASP102 3.4 41.1 1.0 CZ B:TYR25 3.4 21.4 1.0 C B:PHE86 3.5 27.3 1.0 O C:HOH403 3.8 27.8 1.0 CE1 B:TYR25 3.9 19.2 1.0 CA B:THR83 3.9 21.2 1.0 CA B:THR87 4.3 31.2 1.0 N B:THR87 4.3 28.0 1.0 CB B:THR83 4.4 22.0 1.0 CE2 B:TYR25 4.4 19.8 1.0 N B:SER84 4.5 22.4 1.0 OG1 B:THR87 4.6 41.7 1.0 N B:PHE86 4.6 23.0 1.0 CA B:PHE86 4.6 24.4 1.0 CB C:ASP102 4.8 34.9 1.0 CA B:SER84 4.8 22.1 1.0 CD2 B:TYR95 4.9 21.7 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


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 D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:30.1 occ:1.00 O C:THR83 2.3 24.7 1.0 O C:PHE86 2.3 27.8 1.0 O C:HOH414 2.4 35.6 1.0 OH C:TYR25 2.5 27.6 1.0 OD1 D:ASP102 2.6 40.8 1.0 OD2 D:ASP102 3.3 45.6 1.0 CG D:ASP102 3.3 40.8 1.0 C C:THR83 3.4 22.2 1.0 CZ C:TYR25 3.5 22.8 1.0 C C:PHE86 3.6 26.0 1.0 CA C:THR83 3.9 21.7 1.0 CE1 C:TYR25 3.9 19.8 1.0 O D:HOH411 4.0 22.9 1.0 CB C:THR83 4.3 21.4 1.0 CA C:THR87 4.3 30.6 1.0 N C:THR87 4.3 28.2 1.0 CE2 C:TYR25 4.5 19.6 1.0 N C:SER84 4.5 24.1 1.0 OG1 C:THR87 4.6 40.7 1.0 CA C:PHE86 4.6 23.9 1.0 N C:PHE86 4.6 23.2 1.0 CB D:ASP102 4.8 34.7 1.0 CD2 C:TYR95 4.9 20.8 1.0 CA C:SER84 5.0 25.4 1.0 CG2 C:THR83 5.0 22.6 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:33.4 occ:1.00 O D:THR83 2.3 25.2 1.0 O D:HOH423 2.3 34.0 1.0 O D:PHE86 2.3 27.1 1.0 OH D:TYR25 2.5 26.5 1.0 OD1 E:ASP102 2.6 44.1 1.0 OD2 E:ASP102 2.8 44.7 1.0 CG E:ASP102 3.1 41.5 1.0 C D:THR83 3.4 21.2 1.0 CZ D:TYR25 3.5 22.4 1.0 C D:PHE86 3.6 24.0 1.0 CA D:THR83 3.9 19.0 1.0 O E:HOH405 3.9 27.4 1.0 CE2 D:TYR25 3.9 21.7 1.0 CB D:THR83 4.3 19.2 1.0 CA D:THR87 4.4 28.9 1.0 N D:THR87 4.4 27.3 1.0 CE1 D:TYR25 4.4 22.7 1.0 N D:SER84 4.5 22.2 1.0 CB E:ASP102 4.6 33.4 1.0 OG1 D:THR87 4.6 40.8 1.0 CA D:PHE86 4.7 23.1 1.0 N D:PHE86 4.7 23.7 1.0 CD2 D:TYR95 4.9 22.7 1.0 CA D:SER84 5.0 20.6 1.0 CE2 D:TYR95 5.0 22.4 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Crystal Structure of the D116N Mutant of the Light-Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na301 b:33.4 occ:1.00 O E:THR83 2.2 26.9 1.0 O E:HOH426 2.2 39.4 1.0 O E:PHE86 2.3 27.0 1.0 OH E:TYR25 2.5 27.4 1.0 OD1 A:ASP102 2.6 33.0 1.0 C E:THR83 3.3 22.9 1.0 CG A:ASP102 3.3 44.1 1.0 OD2 A:ASP102 3.3 42.2 1.0 CZ E:TYR25 3.5 24.5 1.0 C E:PHE86 3.6 25.5 1.0 O A:HOH412 3.8 19.4 1.0 CA E:THR83 3.9 20.8 1.0 CE1 E:TYR25 3.9 20.5 1.0 CA E:THR87 4.3 29.0 1.0 N E:THR87 4.4 27.2 1.0 CB E:THR83 4.4 20.4 1.0 N E:SER84 4.5 22.9 0.5 N E:SER84 4.5 22.2 0.5 CE2 E:TYR25 4.5 24.3 1.0 OG1 E:THR87 4.6 36.7 1.0 N E:PHE86 4.6 23.6 1.0 CA E:PHE86 4.6 23.6 1.0 CB A:ASP102 4.8 40.5 1.0 CA E:SER84 4.9 23.6 0.5 CA E:SER84 4.9 22.4 0.5 CD2 E:TYR95 4.9 23.6 1.0

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