Sodium in PDB 8rq5: Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2

The binding sites of Sodium atom in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2 (pdb code 8rq5). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2, PDB code: 8rq5:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Na304 b:29.0 occ:1.00 O A:THR83 2.4 27.2 1.0 O A:PHE86 2.4 27.9 1.0 O A:HOH433 2.4 41.0 1.0 OH A:TYR25 2.4 23.6 1.0 OD1 B:ASP102 2.5 38.4 1.0 CG B:ASP102 3.2 39.3 1.0 OD2 B:ASP102 3.2 43.2 1.0 CZ A:TYR25 3.3 22.6 1.0 C A:THR83 3.5 20.9 1.0 O B:HOH402 3.6 21.9 1.0 C A:PHE86 3.6 23.9 1.0 CA A:THR83 3.9 21.0 1.0 CE1 A:TYR25 3.9 22.4 1.0 CE2 A:TYR25 4.2 22.2 1.0 CA A:THR87 4.3 28.5 1.0 CB A:THR83 4.3 24.1 1.0 N A:THR87 4.4 25.2 1.0 CD2 A:TYR95 4.5 25.4 1.0 OG1 A:THR87 4.5 43.2 1.0 CE2 A:TYR95 4.6 26.9 1.0 N A:SER84 4.7 22.5 1.0 CB B:ASP102 4.7 32.6 1.0 N A:PHE86 4.7 24.9 1.0 CA A:PHE86 4.7 24.2 1.0 O A:HOH462 4.8 69.6 1.0

Sodium binding site 2 out of 5 in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na306 b:29.9 occ:1.00 O B:THR83 2.4 28.6 1.0 O B:PHE86 2.4 28.2 1.0 O B:HOH446 2.4 44.5 1.0 OH B:TYR25 2.5 24.6 1.0 OD1 C:ASP102 2.5 39.4 1.0 CG C:ASP102 3.2 40.1 1.0 OD2 C:ASP102 3.2 43.7 1.0 CZ B:TYR25 3.3 23.2 1.0 C B:THR83 3.5 21.1 1.0 O C:HOH402 3.6 22.1 1.0 C B:PHE86 3.6 23.7 1.0 CA B:THR83 3.9 20.9 1.0 CE1 B:TYR25 3.9 23.1 1.0 CE2 B:TYR25 4.2 22.8 1.0 CA B:THR87 4.2 28.3 1.0 CB B:THR83 4.3 23.6 1.0 N B:THR87 4.4 24.8 1.0 CD2 B:TYR95 4.5 25.2 1.0 OG1 B:THR87 4.5 44.5 1.0 CE2 B:TYR95 4.6 26.6 1.0 N B:SER84 4.7 22.8 1.0 CB C:ASP102 4.7 33.1 1.0 N B:PHE86 4.7 24.8 1.0 CA B:PHE86 4.7 24.2 1.0

Sodium binding site 3 out of 5 in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2 within 5.0Å range: probe atom residue distance (Å) B Occ C:Na304 b:29.6 occ:1.00 O C:THR83 2.4 27.9 1.0 O C:PHE86 2.4 28.1 1.0 O C:HOH437 2.5 42.5 1.0 OH C:TYR25 2.5 24.1 1.0 OD1 D:ASP102 2.5 39.3 1.0 CG D:ASP102 3.2 39.9 1.0 OD2 D:ASP102 3.2 44.6 1.0 CZ C:TYR25 3.3 23.0 1.0 C C:THR83 3.5 20.9 1.0 O D:HOH402 3.6 21.6 1.0 C C:PHE86 3.6 24.2 1.0 CA C:THR83 3.9 20.8 1.0 CE1 C:TYR25 3.9 23.0 1.0 CE2 C:TYR25 4.3 22.5 1.0 CA C:THR87 4.3 28.7 1.0 CB C:THR83 4.3 23.6 1.0 N C:THR87 4.4 25.4 1.0 CD2 C:TYR95 4.5 25.4 1.0 OG1 C:THR87 4.5 43.0 1.0 CE2 C:TYR95 4.6 26.8 1.0 N C:SER84 4.6 22.6 1.0 CB D:ASP102 4.7 32.6 1.0 N C:PHE86 4.7 24.8 1.0 CA C:PHE86 4.7 24.4 1.0

Sodium binding site 4 out of 5 in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2 within 5.0Å range: probe atom residue distance (Å) B Occ D:Na305 b:29.6 occ:1.00 O D:THR83 2.4 28.2 1.0 O D:PHE86 2.4 28.4 1.0 OH D:TYR25 2.5 23.7 1.0 O D:HOH431 2.5 42.8 1.0 OD1 E:ASP102 2.5 38.9 1.0 CG E:ASP102 3.2 39.6 1.0 OD2 E:ASP102 3.2 43.8 1.0 CZ D:TYR25 3.3 22.4 1.0 C D:THR83 3.5 21.1 1.0 O E:HOH402 3.6 21.8 1.0 C D:PHE86 3.6 24.1 1.0 CA D:THR83 3.9 20.9 1.0 CE1 D:TYR25 3.9 22.5 1.0 CA D:THR87 4.2 28.1 1.0 CE2 D:TYR25 4.3 22.0 1.0 CB D:THR83 4.3 23.9 1.0 N D:THR87 4.4 25.2 1.0 CD2 D:TYR95 4.5 25.1 1.0 OG1 D:THR87 4.5 42.3 1.0 CE2 D:TYR95 4.6 26.5 1.0 N D:SER84 4.7 22.7 1.0 CB E:ASP102 4.7 32.8 1.0 N D:PHE86 4.7 24.9 1.0 CA D:PHE86 4.7 24.5 1.0

Sodium binding site 5 out of 5 in the Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Cryo-Em Structure of the Light-Driven Sodium-Pumping Rhodopsin KR2 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na306 b:29.1 occ:1.00 O E:PHE86 2.4 27.7 1.0 O E:THR83 2.4 27.7 1.0 O E:HOH440 2.4 42.4 1.0 OH E:TYR25 2.5 23.7 1.0 OD1 A:ASP102 2.5 39.3 1.0 CG A:ASP102 3.2 40.0 1.0 OD2 A:ASP102 3.2 44.1 1.0 CZ E:TYR25 3.3 22.4 1.0 C E:THR83 3.5 20.7 1.0 O A:HOH401 3.6 22.6 1.0 C E:PHE86 3.6 23.9 1.0 CA E:THR83 3.9 20.6 1.0 CE1 E:TYR25 3.9 22.4 1.0 CE2 E:TYR25 4.2 21.9 1.0 CA E:THR87 4.2 28.1 1.0 CB E:THR83 4.3 23.6 1.0 N E:THR87 4.4 25.0 1.0 CD2 E:TYR95 4.5 25.3 1.0 OG1 E:THR87 4.5 42.1 1.0 CE2 E:TYR95 4.6 26.7 1.0 N E:SER84 4.7 22.4 1.0 CB A:ASP102 4.7 32.9 1.0 N E:PHE86 4.7 24.8 1.0 CA E:PHE86 4.7 24.3 1.0

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