Sodium in PDB 6rf4: Crystal Structure of the Potassium-Pumping S254A Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0

The structure of Crystal Structure of the Potassium-Pumping S254A Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rf4 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)	44.91 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.396, 240.045, 135.140, 90.00, 90.00, 90.00
R / Rfree (%)	18.1 / 21.2

The binding sites of Sodium atom in the Crystal Structure of the Potassium-Pumping S254A Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 (pdb code 6rf4). 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 Potassium-Pumping S254A Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rf4:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of the Potassium-Pumping S254A 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 Potassium-Pumping S254A 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:Na309 b:47.4 occ:1.00 O A:HOH427 2.2 35.5 1.0 O A:THR83 2.3 45.5 1.0 O A:PHE86 2.5 44.4 1.0 OD1 B:ASP102 2.5 53.7 1.0 OH A:TYR25 2.6 38.9 1.0 CG B:ASP102 3.2 54.3 1.0 OD2 B:ASP102 3.2 56.5 1.0 C A:THR83 3.4 36.5 1.0 O B:HOH401 3.5 60.7 1.0 O A:HOH447 3.5 58.6 1.0 CZ A:TYR25 3.6 37.5 1.0 O B:HOH415 3.6 38.2 1.0 C A:PHE86 3.6 39.2 1.0 CA A:THR83 3.9 40.5 1.0 CE1 A:TYR25 4.1 36.4 1.0 CA A:THR87 4.2 45.5 1.0 OG1 A:THR87 4.2 53.8 1.0 CB A:THR83 4.3 43.9 1.0 N A:THR87 4.3 44.2 1.0 CE2 A:TYR25 4.5 36.1 1.0 N A:SER84 4.6 37.9 0.5 N A:SER84 4.6 36.6 0.5 CB B:ASP102 4.7 50.1 1.0 N A:PHE86 4.8 33.8 1.0 CA A:PHE86 4.8 36.8 1.0 CD2 A:TYR95 4.8 37.1 1.0 CB A:THR87 4.8 38.1 1.0 O B:SER100 4.9 53.3 1.0 CE2 A:TYR95 5.0 42.3 1.0 CA A:SER84 5.0 37.4 0.5 CA A:SER84 5.0 35.2 0.5

Sodium binding site 2 out of 5 in the Crystal Structure of the Potassium-Pumping S254A 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 Potassium-Pumping S254A 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:Na307 b:41.2 occ:1.00 O B:HOH446 2.3 46.1 1.0 OH B:TYR25 2.3 41.5 1.0 O B:THR83 2.4 46.3 1.0 O B:PHE86 2.4 42.7 1.0 OD1 C:ASP102 2.4 49.4 1.0 O C:HOH445 2.9 66.1 1.0 CG C:ASP102 3.1 53.5 1.0 OD2 C:ASP102 3.1 51.1 1.0 CZ B:TYR25 3.3 38.5 1.0 C B:THR83 3.4 38.3 1.0 C B:PHE86 3.6 39.2 1.0 O C:HOH427 3.7 31.3 1.0 O C:HOH402 3.8 63.0 1.0 CE1 B:TYR25 3.8 40.0 1.0 CA B:THR83 3.8 39.1 1.0 CE2 B:TYR25 4.2 37.1 1.0 O B:HOH463 4.2 59.5 1.0 CA B:THR87 4.2 42.9 1.0 CB B:THR83 4.2 37.0 1.0 N B:THR87 4.4 43.3 1.0 OG1 B:THR87 4.4 53.0 1.0 CB C:ASP102 4.6 45.8 1.0 CD2 B:TYR95 4.6 41.7 1.0 N B:SER84 4.6 38.8 0.5 N B:SER84 4.6 38.3 0.5 CA B:PHE86 4.7 37.9 1.0 N B:PHE86 4.8 36.1 1.0 CE2 B:TYR95 4.8 42.1 1.0 CB B:THR87 5.0 40.5 1.0 CG2 B:THR83 5.0 35.5 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Potassium-Pumping S254A 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 Potassium-Pumping S254A 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:Na320 b:40.2 occ:1.00 O C:HOH434 2.2 51.7 1.0 O C:PHE86 2.3 39.5 1.0 O C:THR83 2.4 37.6 1.0 OH C:TYR25 2.4 40.9 1.0 OD1 D:ASP102 2.5 50.0 1.0 O D:HOH435 2.8 58.5 1.0 CG D:ASP102 3.2 58.9 1.0 OD2 D:ASP102 3.3 52.4 1.0 CZ C:TYR25 3.4 37.0 1.0 C C:THR83 3.4 36.0 1.0 C C:PHE86 3.5 46.3 1.0 O D:HOH421 3.6 38.2 1.0 CA C:THR83 3.8 37.4 1.0 CE1 C:TYR25 3.9 38.8 1.0 O C:HOH461 4.0 50.0 1.0 CA C:THR87 4.1 42.9 1.0 CB C:THR83 4.3 37.5 1.0 N C:THR87 4.3 47.7 1.0 OG1 C:THR87 4.3 60.0 1.0 O D:HOH403 4.3 48.4 1.0 CE2 C:TYR25 4.3 35.6 1.0 N C:SER84 4.6 37.7 0.5 N C:SER84 4.6 36.2 0.5 CA C:PHE86 4.7 41.0 1.0 CD2 C:TYR95 4.7 40.0 1.0 N C:PHE86 4.7 34.4 1.0 CB D:ASP102 4.7 49.8 1.0 CE2 C:TYR95 4.8 42.3 1.0 CB C:THR87 4.9 48.0 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Potassium-Pumping S254A 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 Potassium-Pumping S254A 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:Na310 b:46.4 occ:1.00 O D:HOH423 2.2 48.9 1.0 O D:THR83 2.2 45.8 1.0 O D:PHE86 2.5 44.7 1.0 OH D:TYR25 2.5 39.6 1.0 OD1 E:ASP102 2.5 52.9 1.0 OD2 E:ASP102 3.1 61.9 1.0 CG E:ASP102 3.2 49.1 1.0 C D:THR83 3.3 37.8 1.0 CZ D:TYR25 3.5 34.4 1.0 C D:PHE86 3.6 35.0 1.0 CA D:THR83 3.8 40.0 1.0 O E:HOH414 3.8 36.1 1.0 O D:HOH454 4.0 64.9 1.0 CE1 D:TYR25 4.0 34.9 1.0 CB D:THR83 4.2 39.9 1.0 CA D:THR87 4.2 42.4 1.0 OG1 D:THR87 4.3 51.4 1.0 N D:THR87 4.4 38.5 1.0 CE2 D:TYR25 4.4 39.3 1.0 O E:HOH406 4.4 63.4 1.0 N D:SER84 4.5 36.8 0.5 N D:SER84 4.5 35.2 0.5 CB E:ASP102 4.6 43.0 1.0 N D:PHE86 4.7 34.5 1.0 CA D:PHE86 4.7 35.3 1.0 CD2 D:TYR95 4.8 37.6 1.0 CB D:THR87 4.9 40.1 1.0 CA D:SER84 4.9 38.1 0.5 CE2 D:TYR95 4.9 41.3 1.0 CA D:SER84 5.0 35.4 0.5 CG2 D:THR83 5.0 38.4 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Potassium-Pumping S254A 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 Potassium-Pumping S254A 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:Na309 b:38.3 occ:1.00 O E:HOH433 2.3 46.3 1.0 O E:PHE86 2.4 38.3 1.0 O E:THR83 2.4 49.8 1.0 OH E:TYR25 2.5 42.6 1.0 OD1 A:ASP102 2.5 49.7 1.0 OD2 A:ASP102 3.1 50.4 1.0 CG A:ASP102 3.2 48.0 1.0 CZ E:TYR25 3.4 41.6 1.0 C E:THR83 3.4 39.9 1.0 C E:PHE86 3.6 39.0 1.0 O A:HOH414 3.6 34.6 1.0 CA E:THR83 3.9 41.2 1.0 CE1 E:TYR25 4.0 37.5 1.0 CA E:THR87 4.1 43.0 1.0 OG1 E:THR87 4.3 49.6 1.0 N E:THR87 4.3 42.2 1.0 CB E:THR83 4.3 34.2 1.0 CE2 E:TYR25 4.4 37.7 1.0 N E:SER84 4.6 39.5 0.5 N E:SER84 4.6 37.9 0.5 CB A:ASP102 4.7 37.3 1.0 CA E:PHE86 4.7 36.5 1.0 CD2 E:TYR95 4.7 38.1 1.0 N E:PHE86 4.7 35.0 1.0 CB E:THR87 4.9 41.5 1.0 CE2 E:TYR95 4.9 37.4 1.0 O A:SER100 5.0 44.5 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