Sodium in PDB 6rf0: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form, PDB code: 6rf0 was solved by K.Kovalev, V.Polovinkin, I.Gushchin, V.Borshchevskiy, V.Gordeliy, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.32 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	128.184, 239.719, 131.909, 90.00, 90.00, 90.00
R / Rfree (%)	21.7 / 25.2

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form (pdb code 6rf0). 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 "Dry" Form, PDB code: 6rf0:
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 "Dry" Form


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 "Dry" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:41.0 occ:1.00 O A:PHE86 2.3 34.9 1.0 OD1 B:ASP102 2.5 70.2 1.0 O A:THR83 2.5 33.9 1.0 OH A:TYR25 2.7 38.7 1.0 OD2 B:ASP102 2.9 56.1 1.0 CG B:ASP102 3.1 62.6 1.0 C A:PHE86 3.4 34.0 1.0 CZ A:TYR25 3.6 35.4 1.0 C A:THR83 3.7 32.8 1.0 CE1 A:TYR25 4.0 34.0 1.0 CA A:THR87 4.1 40.0 1.0 N A:THR87 4.2 33.5 1.0 CA A:THR83 4.3 32.2 1.0 N A:PHE86 4.5 35.0 1.0 CE2 A:TYR25 4.5 37.8 1.0 CA A:PHE86 4.5 37.1 1.0 CB B:ASP102 4.6 51.9 1.0 OG1 A:THR87 4.7 52.0 1.0 O B:SER100 4.7 92.6 1.0 N A:SER84 4.8 33.2 1.0 CB A:THR83 4.8 33.6 1.0 CD2 A:TYR95 4.8 38.4 1.0 CB A:THR87 4.9 39.6 1.0 CE2 A:TYR95 4.9 38.7 1.0 C A:SER84 5.0 41.2 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form


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 "Dry" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:35.6 occ:1.00 O E:THR83 2.4 21.6 1.0 O E:PHE86 2.5 29.7 1.0 OD2 A:ASP102 2.7 60.7 1.0 OD1 A:ASP102 2.8 52.8 1.0 OH E:TYR25 3.0 44.5 1.0 CG A:ASP102 3.1 60.0 1.0 C E:THR83 3.6 24.9 1.0 C E:PHE86 3.6 28.7 1.0 CZ E:TYR25 3.9 37.6 1.0 CA E:THR87 4.2 35.0 1.0 CA E:THR83 4.3 25.7 1.0 N E:THR87 4.3 29.6 1.0 CE1 E:TYR25 4.4 37.4 1.0 OG1 E:THR87 4.5 44.1 1.0 N E:SER84 4.6 30.6 1.0 CB A:ASP102 4.6 47.4 1.0 N E:PHE86 4.6 34.9 1.0 O A:SER100 4.6 0.8 1.0 CA E:PHE86 4.7 31.5 1.0 CA E:SER84 4.7 36.7 1.0 CB E:THR83 4.8 25.8 1.0 C E:SER84 4.8 34.3 1.0 CE2 E:TYR25 4.9 38.1 1.0 CB E:THR87 4.9 32.3 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form


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 "Dry" Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:25.2 occ:1.00 O B:THR83 2.2 33.1 1.0 O B:PHE86 2.3 42.1 1.0 OH B:TYR25 2.5 46.4 1.0 OD2 C:ASP102 2.7 61.5 1.0 OD1 C:ASP102 2.9 61.2 1.0 CG C:ASP102 3.1 59.4 1.0 C B:THR83 3.3 29.3 1.0 CZ B:TYR25 3.4 48.9 1.0 C B:PHE86 3.5 39.2 1.0 CE1 B:TYR25 3.9 50.6 1.0 CA B:THR83 3.9 29.0 1.0 CA B:THR87 4.3 43.3 1.0 N B:THR87 4.3 41.2 1.0 N B:PHE86 4.4 39.2 1.0 CE2 B:TYR25 4.4 55.5 1.0 CB B:THR83 4.5 29.2 1.0 N B:SER84 4.5 31.2 1.0 CA B:PHE86 4.5 41.0 1.0 CB C:ASP102 4.6 44.9 1.0 C B:SER84 4.8 37.6 1.0 CA B:SER84 4.9 35.7 1.0 OG1 B:THR87 4.9 50.9 1.0 CD2 B:TYR95 5.0 34.0 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form


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 "Dry" Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na301 b:32.4 occ:1.00 O C:THR83 2.2 37.9 1.0 O C:PHE86 2.3 44.0 1.0 OH C:TYR25 2.5 43.1 1.0 OD1 D:ASP102 3.0 57.5 1.0 OD2 D:ASP102 3.0 42.6 1.0 C C:THR83 3.3 31.1 1.0 CG D:ASP102 3.3 48.3 1.0 CZ C:TYR25 3.4 47.1 1.0 C C:PHE86 3.5 37.4 1.0 CE1 C:TYR25 3.9 45.6 1.0 CA C:THR83 3.9 30.4 1.0 CA C:THR87 4.4 40.6 1.0 N C:THR87 4.4 34.2 1.0 N C:SER84 4.4 35.1 1.0 N C:PHE86 4.4 37.1 1.0 CB C:THR83 4.4 28.8 1.0 CE2 C:TYR25 4.5 46.7 1.0 CA C:PHE86 4.5 40.8 1.0 CA C:SER84 4.7 37.9 1.0 C C:SER84 4.8 40.0 1.0 CB D:ASP102 4.8 41.6 1.0 OG1 C:THR87 4.9 49.9 1.0 CD2 C:TYR95 5.0 37.9 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Dry" Form


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 "Dry" Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:40.2 occ:1.00 O D:THR83 2.4 31.2 1.0 O D:PHE86 2.5 61.5 1.0 OD2 E:ASP102 2.6 52.9 1.0 OD1 E:ASP102 2.8 48.7 1.0 OH D:TYR25 3.0 42.3 1.0 CG E:ASP102 3.0 55.4 1.0 C D:PHE86 3.6 44.1 1.0 C D:THR83 3.6 29.7 1.0 CZ D:TYR25 4.0 42.0 1.0 CA D:THR87 4.1 39.3 1.0 N D:THR87 4.3 42.0 1.0 CA D:THR83 4.4 31.5 1.0 OG1 D:THR87 4.4 44.8 1.0 O E:SER100 4.5 95.0 1.0 CE2 D:TYR25 4.5 47.1 1.0 CB E:ASP102 4.5 42.0 1.0 N D:PHE86 4.6 38.0 1.0 N D:SER84 4.6 30.2 1.0 CA D:PHE86 4.7 37.0 1.0 CA D:SER84 4.8 32.5 1.0 C D:SER84 4.8 35.8 1.0 CB D:THR87 4.8 36.4 1.0 CB D:THR83 4.9 29.8 1.0 O D:SER84 5.0 49.5 1.0 CE1 D:TYR25 5.0 35.6 1.0

K.Kovalev, V.Polovinkin, I.Gushchin, A.Alekseev, V.Shevchenko, V.Borshchevskiy, R.Astashkin, T.Balandin, D.Bratanov, S.Vaganova, A.Popov, V.Chupin, G.Buldt, E.Bamberg, V.Gordeliy. Structure and Mechanisms of Sodium-Pumping KR2 Rhodopsin. Sci Adv V. 5 V2671 2019.
ISSN: ESSN 2375-2548
PubMed: 30989112
DOI: 10.1126/SCIADV.AAV2671