Sodium in PDB 6yc2: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0, PDB code: 6yc2 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 / 2.50
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	135.540, 240.130, 138.580, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 18.8

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 (pdb code 6yc2). 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 Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0, PDB code: 6yc2:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:44.2 occ:1.00 O A:HOH436 2.1 51.4 1.0 O A:THR83 2.1 47.6 1.0 O A:PHE86 2.3 41.3 1.0 OD1 B:ASP102 2.5 41.1 1.0 OH A:TYR25 2.5 39.5 1.0 CG B:ASP102 3.2 44.8 1.0 OD2 B:ASP102 3.3 47.8 1.0 C A:THR83 3.3 37.9 1.0 CZ A:TYR25 3.5 40.4 1.0 C A:PHE86 3.5 42.4 1.0 O B:HOH407 3.7 36.7 1.0 CA A:THR83 3.8 40.2 1.0 CE1 A:TYR25 3.9 37.9 1.0 CA A:THR87 4.3 44.2 1.0 N A:THR87 4.3 43.4 1.0 CB A:THR83 4.4 36.8 1.0 N A:SER84 4.4 40.2 1.0 CE2 A:TYR25 4.4 37.3 1.0 OG1 A:THR87 4.5 49.7 1.0 N A:PHE86 4.6 38.5 1.0 CA A:PHE86 4.6 39.3 1.0 CB B:ASP102 4.7 42.2 1.0 CD2 A:TYR95 4.8 42.9 1.0 CA A:SER84 4.8 40.3 1.0 CE2 A:TYR95 4.9 39.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:39.4 occ:1.00 O C:HOH443 2.2 53.8 1.0 O B:THR83 2.2 46.2 1.0 O B:PHE86 2.3 39.2 1.0 OH B:TYR25 2.4 43.1 1.0 OD1 C:ASP102 2.5 39.8 1.0 CG C:ASP102 3.2 43.9 1.0 OD2 C:ASP102 3.2 41.9 1.0 CZ B:TYR25 3.3 42.6 1.0 C B:THR83 3.3 36.3 1.0 C B:PHE86 3.5 41.2 1.0 O C:HOH414 3.8 41.6 1.0 CE1 B:TYR25 3.8 38.3 1.0 CA B:THR83 3.8 39.6 1.0 CE2 B:TYR25 4.3 40.3 1.0 CA B:THR87 4.3 41.6 1.0 N B:THR87 4.3 41.5 1.0 CB B:THR83 4.3 33.6 1.0 N B:SER84 4.5 36.0 1.0 CA B:PHE86 4.6 38.9 1.0 OG1 B:THR87 4.6 53.2 1.0 N B:PHE86 4.6 35.2 1.0 CB C:ASP102 4.7 44.6 1.0 CD2 B:TYR95 4.7 40.7 1.0 CE2 B:TYR95 4.8 42.9 1.0 CA B:SER84 4.9 40.0 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:44.4 occ:1.00 O C:HOH441 2.2 49.8 1.0 O C:THR83 2.2 37.8 1.0 O C:PHE86 2.3 39.1 1.0 OD1 D:ASP102 2.5 41.8 1.0 OH C:TYR25 2.5 41.1 1.0 CG D:ASP102 3.2 47.3 1.0 OD2 D:ASP102 3.3 42.9 1.0 C C:THR83 3.4 36.0 1.0 CZ C:TYR25 3.4 37.2 1.0 C C:PHE86 3.5 41.4 1.0 O D:HOH611 3.6 38.2 1.0 CA C:THR83 3.9 41.2 1.0 CE1 C:TYR25 3.9 41.6 1.0 CA C:THR87 4.2 44.3 1.0 N C:THR87 4.2 40.1 1.0 CE2 C:TYR25 4.4 38.1 1.0 CB C:THR83 4.5 35.7 1.0 OG1 C:THR87 4.5 47.7 1.0 N C:SER84 4.5 36.1 1.0 CA C:PHE86 4.6 39.6 1.0 N C:PHE86 4.6 38.4 1.0 CB D:ASP102 4.7 42.1 1.0 CD2 C:TYR95 4.7 41.0 1.0 CE2 C:TYR95 4.8 41.7 1.0 CA C:SER84 4.9 38.9 1.0 CB C:THR87 5.0 44.2 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na503 b:40.8 occ:1.00 O D:HOH636 2.2 52.9 1.0 O D:THR83 2.3 49.4 1.0 OD1 E:ASP102 2.3 40.5 1.0 O D:PHE86 2.4 43.4 1.0 OH D:TYR25 2.4 40.7 1.0 CG E:ASP102 3.0 50.7 1.0 OD2 E:ASP102 3.1 42.7 1.0 O E:HOH937 3.2 83.1 1.0 CZ D:TYR25 3.3 40.1 1.0 C D:THR83 3.4 41.9 1.0 C D:PHE86 3.6 42.3 1.0 O E:HOH907 3.6 32.8 1.0 CE1 D:TYR25 3.9 42.8 1.0 CA D:THR83 3.9 42.6 1.0 CE2 D:TYR25 4.3 41.4 1.0 CA D:THR87 4.3 40.8 1.0 N D:THR87 4.4 43.8 1.0 CB D:THR83 4.4 36.0 1.0 CB E:ASP102 4.5 41.5 1.0 O D:HOH651 4.6 62.7 1.0 N D:SER84 4.6 38.0 1.0 OG1 D:THR87 4.6 41.5 1.0 CD2 D:TYR95 4.7 42.6 1.0 CA D:PHE86 4.7 38.1 1.0 N D:PHE86 4.7 40.6 1.0 CE2 D:TYR95 4.8 45.5 1.0 CA D:SER84 5.0 44.1 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, 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 Light-Driven Sodium Pump KR2 in the Pentameric Form at Room Temperature, pH 8.0 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na803 b:41.8 occ:1.00 OD1 A:ASP102 2.3 44.9 1.0 O E:HOH925 2.3 49.5 1.0 O E:THR83 2.4 39.9 1.0 O E:PHE86 2.4 42.0 1.0 OH E:TYR25 2.4 40.0 1.0 CG A:ASP102 3.0 45.1 1.0 OD2 A:ASP102 3.1 42.7 1.0 CZ E:TYR25 3.3 41.9 1.0 C E:THR83 3.5 36.8 1.0 O A:HOH407 3.5 35.0 1.0 C E:PHE86 3.6 41.1 1.0 CE1 E:TYR25 3.9 47.5 1.0 O A:HOH411 3.9 66.0 1.0 CA E:THR83 4.0 37.0 1.0 CE2 E:TYR25 4.2 42.0 1.0 CA E:THR87 4.3 41.4 1.0 N E:THR87 4.3 39.4 1.0 CB E:THR83 4.4 37.6 1.0 CB A:ASP102 4.5 40.8 1.0 OG1 E:THR87 4.6 49.1 1.0 CD2 E:TYR95 4.6 39.5 1.0 N E:SER84 4.6 39.2 1.0 CE2 E:TYR95 4.7 37.9 1.0 CA E:PHE86 4.7 38.6 1.0 N E:PHE86 4.8 38.7 1.0

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