Sodium in PDB 9i6h: Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity

The structure of Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity, PDB code: 9i6h was solved by D.Zabelskii, E.Round, H.Han, D.Von Stetten, D.Melo, R.De Wijn, R.Bean, A.Round, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	69.25 / 3.00
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	136.1, 240.9, 138.5, 90, 90, 90
R / Rfree (%)	17.1 / 20.3

The binding sites of Sodium atom in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity (pdb code 9i6h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 5 binding sites of Sodium where determined in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity, PDB code: 9i6h:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:42.9 occ:1.00 O A:PHE86 2.4 45.6 1.0 O A:THR83 2.6 54.6 1.0 O A:HOH421 2.7 62.1 1.0 OD1 B:ASP102 2.7 56.6 1.0 OH A:TYR25 2.9 41.7 1.0 OD2 B:ASP102 3.4 51.7 1.0 O B:HOH410 3.4 46.8 1.0 CG B:ASP102 3.4 44.8 1.0 C A:PHE86 3.5 48.5 1.0 C A:THR83 3.7 51.3 1.0 CZ A:TYR25 3.9 47.6 1.0 CA A:THR87 4.0 46.0 1.0 OG1 A:THR87 4.1 41.5 1.0 N A:THR87 4.2 42.7 1.0 CA A:THR83 4.3 49.1 1.0 CE1 A:TYR25 4.5 48.8 1.0 N A:PHE86 4.5 42.7 1.0 CA A:PHE86 4.6 49.6 1.0 O B:SER100 4.6 46.1 1.0 CB A:THR87 4.6 41.7 1.0 N A:SER84 4.8 47.1 1.0 CB A:THR83 4.8 48.7 1.0 CE2 A:TYR25 4.8 42.6 1.0 CB B:ASP102 4.8 39.4 1.0 CA A:SER84 5.0 47.6 1.0

Sodium binding site 2 out of 5 in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ B:Na302 b:38.3 occ:1.00 O B:THR83 2.4 41.3 1.0 O B:PHE86 2.5 43.0 1.0 OD1 C:ASP102 2.6 54.3 1.0 OH B:TYR25 2.8 43.4 1.0 O B:HOH432 2.9 57.6 1.0 OD2 C:ASP102 3.0 42.4 1.0 CG C:ASP102 3.2 39.8 1.0 C B:THR83 3.5 43.8 1.0 C B:PHE86 3.6 44.0 1.0 O C:HOH406 3.6 51.2 1.0 CZ B:TYR25 3.8 45.9 1.0 OG1 B:THR87 4.1 50.3 1.0 CA B:THR83 4.1 43.1 1.0 CA B:THR87 4.2 41.3 1.0 CE1 B:TYR25 4.3 45.5 1.0 N B:THR87 4.3 40.6 1.0 CB B:THR83 4.6 35.6 1.0 N B:PHE86 4.6 42.7 1.0 N B:SER84 4.6 42.8 1.0 CB C:ASP102 4.7 37.0 1.0 CA B:PHE86 4.7 45.4 1.0 CE2 B:TYR25 4.7 39.5 1.0 CB B:THR87 4.8 41.7 1.0 CA B:SER84 4.9 45.5 1.0 O C:SER100 4.9 56.7 1.0

Sodium binding site 3 out of 5 in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:42.0 occ:1.00 O C:THR83 2.3 44.6 1.0 O C:PHE86 2.4 45.6 1.0 O C:HOH418 2.5 47.1 1.0 OD1 D:ASP102 2.6 48.4 1.0 OH C:TYR25 2.7 46.7 1.0 OD2 D:ASP102 2.9 52.0 1.0 CG D:ASP102 3.1 47.7 1.0 O D:HOH433 3.1 54.6 1.0 C C:THR83 3.4 43.3 1.0 C C:PHE86 3.6 43.4 1.0 CZ C:TYR25 3.7 46.1 1.0 O D:HOH406 3.7 48.6 1.0 CA C:THR83 4.0 42.0 1.0 CE1 C:TYR25 4.2 47.4 1.0 CA C:THR87 4.2 44.2 1.0 N C:THR87 4.3 46.6 1.0 OG1 C:THR87 4.4 51.0 1.0 N C:SER84 4.5 43.3 1.0 CB C:THR83 4.6 37.6 1.0 N C:PHE86 4.6 45.4 1.0 CB D:ASP102 4.6 44.7 1.0 CE2 C:TYR25 4.6 48.8 1.0 CA C:PHE86 4.7 44.0 1.0 CA C:SER84 4.8 43.3 1.0 CD2 C:TYR95 4.8 46.0 1.0 CB C:THR87 4.9 48.8 1.0 O D:SER100 5.0 58.3 1.0 CE2 C:TYR95 5.0 45.1 1.0

Sodium binding site 4 out of 5 in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:42.6 occ:1.00 O D:PHE86 2.3 44.4 1.0 O D:THR83 2.3 45.7 1.0 O D:HOH415 2.7 48.2 1.0 OH D:TYR25 2.7 44.2 1.0 OD1 E:ASP102 2.8 52.9 1.0 OD2 E:ASP102 3.1 47.2 1.0 O E:HOH434 3.3 56.5 1.0 CG E:ASP102 3.3 48.2 1.0 C D:THR83 3.5 44.4 1.0 O E:HOH403 3.5 49.1 1.0 C D:PHE86 3.5 44.2 1.0 CZ D:TYR25 3.8 41.0 1.0 CA D:THR83 4.0 44.9 1.0 CA D:THR87 4.1 42.6 1.0 N D:THR87 4.2 40.7 1.0 CE1 D:TYR25 4.3 42.0 1.0 OG1 D:THR87 4.3 47.7 1.0 N D:PHE86 4.5 43.7 1.0 CB D:THR83 4.5 41.5 1.0 N D:SER84 4.5 43.2 1.0 CA D:PHE86 4.6 45.9 1.0 CE2 D:TYR25 4.7 44.7 1.0 O D:HOH440 4.8 65.7 1.0 CA D:SER84 4.8 48.0 1.0 CB E:ASP102 4.8 40.6 1.0 O E:SER100 4.8 53.3 1.0 CB D:THR87 4.9 42.5 1.0

Sodium binding site 5 out of 5 in the Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 5 of Room Temperature Structure of KR2 Rhodopsin in Pentameric Form at 95% Relative Humidity within 5.0Å range: probe atom residue distance (Å) B Occ E:Na302 b:39.4 occ:1.00 O E:HOH428 2.3 52.8 1.0 OH E:TYR25 2.3 45.6 1.0 O E:THR83 2.4 43.3 1.0 O E:PHE86 2.4 41.2 1.0 OD1 A:ASP102 2.5 51.6 1.0 OD2 A:ASP102 2.8 41.8 1.0 CG A:ASP102 3.0 41.8 1.0 CZ E:TYR25 3.4 43.4 1.0 C E:THR83 3.5 41.0 1.0 O E:HOH432 3.6 52.9 1.0 C E:PHE86 3.6 42.8 1.0 O A:HOH407 3.8 42.4 1.0 CE1 E:TYR25 3.9 39.8 1.0 CA E:THR83 4.0 42.0 1.0 CA E:THR87 4.1 48.1 1.0 CG2 E:THR87 4.2 46.5 1.0 CE2 E:TYR25 4.3 44.0 1.0 N E:THR87 4.3 44.5 1.0 CB E:THR83 4.4 40.9 1.0 CB A:ASP102 4.5 36.2 1.0 N E:SER84 4.6 41.4 1.0 CB E:THR87 4.7 44.6 1.0 N E:PHE86 4.7 38.1 1.0 CA E:PHE86 4.7 43.3 1.0 CD2 E:TYR95 4.8 38.1 1.0 CE2 E:TYR95 4.9 38.1 1.0 CA E:SER84 4.9 44.6 1.0

D.Zabelskii, E.Round, H.Han, D.Von Stetten, R.Letrun, C.Kim, T.Sato, D.Melo, R.De Wijn, K.Kharitonov, P.Smyth, K.Doerner, M.Kloos, T.Dietze, L.Lopez, R.Bean, A.Round. Viscoelastic Characterization of the Lipid Cubic Phase Provides Insights Into High-Viscosity Extrusion Injection For Xfel Experiments. To Be Published.