Sodium in PDB 6rf3: Crystal Structure of the Potassium-Pumping G263F Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0

The structure of Crystal Structure of the Potassium-Pumping G263F Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rf3 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)	47.97 / 2.40
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	131.680, 239.685, 134.584, 90.00, 90.00, 90.00
R / Rfree (%)	17.3 / 20.5

The binding sites of Sodium atom in the Crystal Structure of the Potassium-Pumping G263F Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0 (pdb code 6rf3). 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 G263F Mutant of the Light- Driven Sodium Pump KR2 in the Pentameric Form, pH 8.0, PDB code: 6rf3:
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 G263F 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 G263F 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:Na319 b:45.6 occ:1.00 O A:THR83 2.4 44.9 1.0 O A:HOH442 2.4 35.6 1.0 OD1 B:ASP102 2.4 44.0 1.0 O A:PHE86 2.4 39.9 1.0 OH A:TYR25 2.6 36.6 1.0 O B:HOH451 3.1 58.6 1.0 CG B:ASP102 3.2 48.8 1.0 OD2 B:ASP102 3.3 50.2 1.0 O B:HOH440 3.4 30.7 1.0 C A:THR83 3.4 36.0 1.0 CZ A:TYR25 3.6 35.4 1.0 O B:HOH404 3.6 52.2 1.0 C A:PHE86 3.6 37.9 1.0 O A:HOH490 3.9 56.5 1.0 CA A:THR83 4.0 35.0 1.0 CA A:THR87 4.1 42.9 1.0 CE1 A:TYR25 4.2 38.2 1.0 OG1 A:THR87 4.2 46.0 1.0 N A:THR87 4.3 39.0 1.0 CB A:THR83 4.4 38.0 1.0 CE2 A:TYR25 4.5 35.1 1.0 N A:SER84 4.6 35.1 1.0 CB B:ASP102 4.6 43.9 1.0 CB A:THR87 4.8 38.0 1.0 CD2 A:TYR95 4.8 37.3 1.0 CA A:PHE86 4.8 34.7 1.0 N A:PHE86 4.8 31.4 1.0 O B:SER100 4.8 44.4 1.0 CE2 A:TYR95 4.9 40.0 1.0 CA A:SER84 5.0 36.8 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of the Potassium-Pumping G263F 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 G263F 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:Na320 b:39.4 occ:1.00 O B:THR83 2.3 48.9 1.0 OH B:TYR25 2.3 35.1 1.0 O B:PHE86 2.4 41.4 1.0 OD1 C:ASP102 2.4 38.3 1.0 O B:HOH448 2.4 35.9 1.0 O C:HOH436 2.7 59.3 1.0 CG C:ASP102 3.2 43.3 1.0 CZ B:TYR25 3.3 38.9 1.0 C B:THR83 3.4 39.6 1.0 OD2 C:ASP102 3.4 48.0 1.0 C B:PHE86 3.6 39.5 1.0 O C:HOH427 3.7 33.5 1.0 O C:HOH401 3.8 57.4 1.0 CA B:THR83 3.8 34.3 1.0 CE1 B:TYR25 3.9 38.5 1.0 O B:HOH478 4.1 61.7 1.0 CA B:THR87 4.2 39.0 1.0 CB B:THR83 4.2 35.6 1.0 CE2 B:TYR25 4.3 35.4 1.0 N B:THR87 4.3 41.4 1.0 OG1 B:THR87 4.3 47.7 1.0 N B:SER84 4.5 35.7 1.0 CB C:ASP102 4.7 35.4 1.0 CD2 B:TYR95 4.7 39.9 1.0 CA B:PHE86 4.7 41.2 1.0 N B:PHE86 4.7 35.0 1.0 CE2 B:TYR95 4.9 39.6 1.0 CB B:THR87 4.9 38.2 1.0 CA B:SER84 5.0 37.8 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of the Potassium-Pumping G263F 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 G263F 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:42.4 occ:1.00 O C:THR83 2.3 41.0 1.0 O C:HOH426 2.3 38.1 1.0 O C:PHE86 2.4 45.8 1.0 OD1 D:ASP102 2.4 43.5 1.0 OH C:TYR25 2.6 39.8 1.0 O D:HOH435 2.9 56.3 1.0 CG D:ASP102 3.3 44.0 1.0 C C:THR83 3.4 39.4 1.0 OD2 D:ASP102 3.4 53.9 1.0 C C:PHE86 3.5 45.1 1.0 O D:HOH432 3.5 27.2 1.0 CZ C:TYR25 3.5 33.9 1.0 O C:HOH483 3.9 58.7 1.0 CA C:THR83 3.9 40.0 1.0 O D:HOH402 4.0 56.9 1.0 CA C:THR87 4.1 42.1 1.0 CE1 C:TYR25 4.1 37.9 1.0 OG1 C:THR87 4.1 51.2 1.0 N C:THR87 4.2 44.0 1.0 CB C:THR83 4.3 38.3 1.0 CE2 C:TYR25 4.5 33.8 1.0 N C:SER84 4.5 35.4 1.0 CA C:PHE86 4.7 41.5 1.0 N C:PHE86 4.7 35.6 1.0 CB D:ASP102 4.7 39.8 1.0 CB C:THR87 4.8 43.6 1.0 CD2 C:TYR95 4.8 41.2 1.0 CA C:SER84 4.9 37.8 1.0 CE2 C:TYR95 5.0 38.5 1.0 O D:SER100 5.0 41.2 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of the Potassium-Pumping G263F 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 G263F 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:Na316 b:41.0 occ:1.00 O D:THR83 2.3 47.9 1.0 O D:HOH427 2.3 38.1 1.0 O D:PHE86 2.3 41.5 1.0 OD1 E:ASP102 2.5 35.8 1.0 OH D:TYR25 2.5 36.8 1.0 O E:HOH460 2.8 68.0 1.0 CG E:ASP102 3.3 40.3 1.0 C D:THR83 3.3 39.6 1.0 OD2 E:ASP102 3.4 46.6 1.0 CZ D:TYR25 3.5 39.5 1.0 C D:PHE86 3.5 37.1 1.0 O E:HOH413 3.6 30.9 1.0 CA D:THR83 3.9 41.0 1.0 O D:HOH479 3.9 61.0 1.0 CE1 D:TYR25 4.0 38.3 1.0 CA D:THR87 4.1 42.3 1.0 OG1 D:THR87 4.1 53.4 1.0 O E:HOH404 4.2 52.5 1.0 N D:THR87 4.2 37.8 1.0 CB D:THR83 4.3 39.1 1.0 CE2 D:TYR25 4.4 40.0 1.0 N D:SER84 4.5 35.9 1.0 CA D:PHE86 4.6 39.3 1.0 N D:PHE86 4.6 39.1 1.0 CD2 D:TYR95 4.7 41.8 1.0 CB E:ASP102 4.7 38.8 1.0 CB D:THR87 4.7 40.0 1.0 CA D:SER84 4.9 40.2 1.0 CE2 D:TYR95 4.9 37.3 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of the Potassium-Pumping G263F 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 G263F 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:Na320 b:38.3 occ:1.00 O E:THR83 2.4 41.9 1.0 OD1 A:ASP102 2.4 42.9 1.0 O E:HOH447 2.4 38.3 1.0 OH E:TYR25 2.4 37.4 1.0 O E:PHE86 2.4 38.8 1.0 O A:HOH452 2.8 57.5 1.0 CG A:ASP102 3.1 40.7 1.0 OD2 A:ASP102 3.2 43.6 1.0 CZ E:TYR25 3.4 35.7 1.0 C E:THR83 3.4 39.5 1.0 C E:PHE86 3.6 37.5 1.0 O A:HOH421 3.7 32.2 1.0 O E:HOH481 3.7 60.6 1.0 CA E:THR83 3.9 35.7 1.0 CE1 E:TYR25 4.0 36.6 1.0 CA E:THR87 4.2 38.0 1.0 CB E:THR83 4.2 33.3 1.0 O A:HOH404 4.3 62.7 1.0 OG1 E:THR87 4.3 41.3 1.0 CE2 E:TYR25 4.3 33.0 1.0 N E:THR87 4.4 37.5 1.0 CB A:ASP102 4.6 37.4 1.0 N E:SER84 4.6 36.0 1.0 CD2 E:TYR95 4.7 37.2 1.0 CA E:PHE86 4.8 36.3 1.0 N E:PHE86 4.8 34.0 1.0 CE2 E:TYR95 4.9 38.0 1.0 CB E:THR87 4.9 38.3 1.0 O E:HOH491 4.9 59.9 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