Sodium in PDB 6rf1: Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form

The structure of Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form, PDB code: 6rf1 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)	48.17 / 2.80
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	130.628, 240.474, 135.614, 90.00, 90.00, 90.00
R / Rfree (%)	18.8 / 22.3

The binding sites of Sodium atom in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" Form (pdb code 6rf1). 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 "Wet" Form, PDB code: 6rf1:
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 "Wet" 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 "Wet" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na310 b:46.0 occ:1.00 O A:THR83 2.3 52.4 1.0 O A:HOH421 2.3 47.8 1.0 OD1 B:ASP102 2.5 64.1 1.0 O A:PHE86 2.5 58.0 1.0 OH A:TYR25 2.6 50.2 1.0 O A:HOH429 3.1 58.2 1.0 CG B:ASP102 3.2 64.6 1.0 OD2 B:ASP102 3.3 62.4 1.0 C A:THR83 3.4 48.7 1.0 O B:HOH414 3.5 64.2 1.0 CZ A:TYR25 3.6 49.3 1.0 O A:HOH416 3.6 48.1 1.0 C A:PHE86 3.7 53.6 1.0 CA A:THR83 3.9 49.8 1.0 CA A:THR87 4.2 50.4 1.0 CE1 A:TYR25 4.2 51.5 1.0 OG1 A:THR87 4.2 52.2 1.0 CB A:THR83 4.3 44.7 1.0 N A:THR87 4.3 48.6 1.0 N A:SER84 4.5 45.2 0.5 N A:SER84 4.5 43.4 0.5 CE2 A:TYR25 4.5 46.2 1.0 CB B:ASP102 4.7 62.7 1.0 N A:PHE86 4.8 47.8 1.0 CA A:PHE86 4.8 49.7 1.0 CB A:THR87 4.8 43.7 1.0 O B:SER100 4.9 66.7 1.0 CD2 A:TYR95 4.9 43.3 1.0 CA A:SER84 4.9 50.5 0.5 CA A:SER84 4.9 47.2 0.5

Sodium binding site 2 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" 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 "Wet" Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na314 b:48.5 occ:1.00 O E:THR83 2.4 66.0 1.0 OD1 A:ASP102 2.4 61.4 1.0 O E:PHE86 2.4 44.6 1.0 OH E:TYR25 2.7 54.2 1.0 CG A:ASP102 3.3 54.3 1.0 OD2 A:ASP102 3.5 56.0 1.0 C E:THR83 3.5 62.6 1.0 C E:PHE86 3.6 45.2 1.0 O E:HOH417 3.6 45.5 1.0 CZ E:TYR25 3.7 48.3 1.0 CA E:THR87 4.0 53.1 1.0 OG1 E:THR87 4.1 53.3 1.0 CA E:THR83 4.1 54.4 1.0 N E:THR87 4.2 48.9 1.0 CE1 E:TYR25 4.3 50.0 1.0 CB E:THR83 4.5 47.0 1.0 N E:SER84 4.6 54.4 0.5 N E:SER84 4.6 56.2 0.5 CE2 E:TYR25 4.6 49.1 1.0 CB E:THR87 4.6 44.7 1.0 O A:SER100 4.7 66.0 1.0 CB A:ASP102 4.7 55.3 1.0 CA E:PHE86 4.7 42.6 1.0 N E:PHE86 4.7 48.4 1.0 CD2 E:TYR95 4.9 39.5 1.0 CA E:SER84 5.0 53.6 0.5 CA E:SER84 5.0 56.6 0.5 N A:ASP102 5.0 47.5 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" 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 "Wet" Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na310 b:53.4 occ:1.00 O B:HOH431 2.2 50.7 1.0 OD1 C:ASP102 2.3 59.9 1.0 OH B:TYR25 2.4 44.0 1.0 O B:THR83 2.4 72.7 1.0 O B:PHE86 2.6 45.3 1.0 CG C:ASP102 3.0 60.9 1.0 OD2 C:ASP102 3.1 70.7 1.0 CZ B:TYR25 3.4 48.1 1.0 C B:THR83 3.4 54.5 1.0 O C:HOH414 3.5 56.3 1.0 O C:HOH424 3.6 38.8 1.0 C B:PHE86 3.8 47.7 1.0 CA B:THR83 3.9 51.3 1.0 CE1 B:TYR25 4.0 47.3 1.0 CB B:THR83 4.3 56.1 1.0 CA B:THR87 4.3 48.9 1.0 CE2 B:TYR25 4.3 47.3 1.0 OG1 B:THR87 4.4 50.0 1.0 N B:THR87 4.5 48.2 1.0 CB C:ASP102 4.5 52.9 1.0 N B:SER84 4.6 53.6 0.5 N B:SER84 4.6 52.6 0.5 CD2 B:TYR95 4.8 46.9 1.0 O B:HOH435 4.8 55.3 1.0 O C:SER100 4.8 55.8 1.0 CA B:PHE86 4.9 48.4 1.0 CE2 B:TYR95 4.9 53.1 1.0 N B:PHE86 4.9 53.6 1.0 CG2 B:THR83 4.9 53.9 1.0 N C:ASP102 5.0 54.4 1.0 CB B:THR87 5.0 44.5 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" 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 "Wet" Form within 5.0Å range: probe atom residue distance (Å) B Occ C:Na315 b:44.8 occ:1.00 O C:HOH409 2.1 40.0 1.0 O C:THR83 2.3 45.6 1.0 OD1 D:ASP102 2.4 50.4 1.0 O C:PHE86 2.5 48.0 1.0 OH C:TYR25 2.6 58.0 1.0 O D:HOH427 2.9 64.5 1.0 CG D:ASP102 3.2 54.6 1.0 OD2 D:ASP102 3.3 62.3 1.0 C C:THR83 3.4 47.4 1.0 O D:HOH421 3.4 33.6 1.0 CZ C:TYR25 3.6 53.6 1.0 O D:HOH401 3.6 69.0 1.0 C C:PHE86 3.7 54.3 1.0 O C:HOH441 3.7 49.9 1.0 CA C:THR83 4.0 45.0 1.0 CA C:THR87 4.1 51.1 1.0 CE1 C:TYR25 4.2 56.1 1.0 OG1 C:THR87 4.2 55.7 1.0 N C:THR87 4.3 51.5 1.0 CB C:THR83 4.4 45.7 1.0 CE2 C:TYR25 4.5 51.3 1.0 N C:SER84 4.6 48.1 0.5 N C:SER84 4.6 48.6 0.5 CB D:ASP102 4.6 48.1 1.0 CB C:THR87 4.8 55.3 1.0 N C:PHE86 4.8 42.8 1.0 O D:SER100 4.8 61.7 1.0 CA C:PHE86 4.8 47.8 1.0 CD2 C:TYR95 4.9 50.7 1.0 CA C:SER84 5.0 54.8 0.5 CA C:SER84 5.0 55.8 0.5 N D:ASP102 5.0 51.8 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Light-Driven Sodium Pump KR2 in the Pentameric "Wet" 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 "Wet" Form within 5.0Å range: probe atom residue distance (Å) B Occ D:Na314 b:58.7 occ:1.00 O D:HOH414 2.1 67.3 1.0 O D:PHE86 2.3 51.6 1.0 OD1 E:ASP102 2.3 64.5 1.0 OH D:TYR25 2.6 48.6 1.0 O D:THR83 2.6 46.3 1.0 CG E:ASP102 3.2 62.5 1.0 O E:HOH420 3.3 38.2 1.0 O E:HOH404 3.3 68.2 1.0 C D:PHE86 3.4 52.1 1.0 OD2 E:ASP102 3.4 71.2 1.0 CZ D:TYR25 3.5 51.1 1.0 C D:THR83 3.7 49.0 1.0 CA D:THR87 3.9 47.5 1.0 CE1 D:TYR25 4.0 51.8 1.0 N D:THR87 4.1 48.0 1.0 OG1 D:THR87 4.1 56.8 1.0 CA D:THR83 4.2 53.0 1.0 CE2 D:TYR25 4.4 57.1 1.0 CD2 D:TYR95 4.5 50.6 1.0 CB E:ASP102 4.6 59.2 1.0 CB D:THR83 4.6 50.9 1.0 CB D:THR87 4.6 46.4 1.0 CA D:PHE86 4.6 52.6 1.0 CE2 D:TYR95 4.7 52.2 1.0 N D:PHE86 4.7 48.5 1.0 N D:SER84 4.8 45.3 0.5 N D:SER84 4.8 46.0 0.5 C D:THR87 4.9 50.0 1.0 N D:PHE88 4.9 50.2 1.0 O E:SER100 4.9 61.6 1.0 N E:ASP102 4.9 49.5 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