Sodium in PDB 6tv7: Crystal Structure of Rsgcamp in the Off State (Illuminated)

The structure of Crystal Structure of Rsgcamp in the Off State (Illuminated), PDB code: 6tv7 was solved by R.Janowski, J.P.Fuenzalida-Werner, K.Mishra, A.C.Stiel, D.Niessing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.09 / 2.90
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	120.67, 120.67, 96.02, 90, 90, 90
R / Rfree (%)	18.2 / 25

The structure of Crystal Structure of Rsgcamp in the Off State (Illuminated) also contains other interesting chemical elements:

Calcium

(Ca)

4 atoms

The binding sites of Sodium atom in the Crystal Structure of Rsgcamp in the Off State (Illuminated) (pdb code 6tv7). 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 Rsgcamp in the Off State (Illuminated), PDB code: 6tv7:
Jump to Sodium binding site number: 1; 2; 3; 4; 5;

Sodium binding site 1 out of 5 in the Crystal Structure of Rsgcamp in the Off State (Illuminated)


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 Rsgcamp in the Off State (Illuminated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na505 b:38.6 occ:1.00 CE A:LYS265 3.5 77.1 1.0 O A:LYS265 3.7 55.1 1.0 O A:GLU282 4.1 43.0 1.0 C A:LYS265 4.3 49.7 1.0 CD A:LYS265 4.3 65.8 1.0 CB A:LYS284 4.3 63.5 1.0 CB A:GLU282 4.3 67.7 1.0 C A:GLU282 4.4 47.8 1.0 CB A:ARG267 4.5 49.4 1.0 N A:ARG267 4.5 45.4 1.0 CB A:LYS265 4.5 51.9 1.0 NZ A:LYS265 4.6 74.6 1.0 N A:LYS284 4.7 54.2 1.0 C A:THR266 4.7 44.8 1.0 N A:THR266 4.8 49.0 1.0 CA A:THR266 4.8 44.8 1.0 N A:LEU283 4.8 47.6 1.0 C A:LEU283 4.9 51.4 1.0 CA A:LEU283 4.9 47.4 1.0 CG A:LYS265 5.0 63.6 1.0

Sodium binding site 2 out of 5 in the Crystal Structure of Rsgcamp in the Off State (Illuminated)


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 Rsgcamp in the Off State (Illuminated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na506 b:37.2 occ:1.00 O A:LEU283 3.6 51.0 1.0 CB A:ASP179 4.0 47.8 1.0 O A:ASP177 4.0 50.0 1.0 N A:ASP179 4.2 48.6 1.0 C A:GLY178 4.5 50.5 1.0 C A:LEU283 4.6 51.4 1.0 C A:ASP177 4.7 51.2 1.0 CB A:GLU282 4.8 67.7 1.0 CA A:ASP179 4.8 46.7 1.0 CA A:GLY178 4.8 51.7 1.0 N A:LEU283 4.9 47.6 1.0 N A:GLY178 5.0 50.1 1.0

Sodium binding site 3 out of 5 in the Crystal Structure of Rsgcamp in the Off State (Illuminated)


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 Rsgcamp in the Off State (Illuminated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na507 b:52.3 occ:1.00 O A:HOH639 3.0 51.5 1.0 O A:ALA245 3.1 57.1 1.0 N A:GLY102 3.6 57.1 1.0 O A:GLY102 3.6 53.0 1.0 OE1 A:GLU248 3.8 88.9 1.0 C A:GLY102 3.8 60.7 1.0 CA A:GLY102 3.8 63.0 1.0 O A:GLY249 3.9 49.6 1.0 CB A:PRO100 3.9 44.5 1.0 C A:ALA245 4.0 49.5 1.0 CA A:ALA245 4.1 47.3 1.0 CD A:GLU248 4.1 92.3 1.0 CB A:GLU248 4.2 73.4 1.0 O A:GLY104 4.3 94.5 1.0 N A:ILE101 4.3 47.1 1.0 CG1 A:VAL106 4.3 54.2 1.0 N A:GLY104 4.4 82.0 1.0 OE2 A:GLU248 4.4 83.8 1.0 CB A:ALA245 4.5 49.7 1.0 N A:ASP103 4.6 74.2 1.0 CA A:GLY104 4.6 81.8 1.0 N A:GLY249 4.7 51.0 1.0 C A:ILE101 4.7 52.1 1.0 CA A:PRO100 4.8 47.5 1.0 CG A:GLU248 4.8 84.8 1.0 C A:PRO100 4.8 46.7 1.0 C A:GLY104 4.9 86.6 1.0

Sodium binding site 4 out of 5 in the Crystal Structure of Rsgcamp in the Off State (Illuminated)


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 Rsgcamp in the Off State (Illuminated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na508 b:43.7 occ:1.00 N A:LYS69 2.9 50.9 1.0 N A:GLN70 3.3 58.5 1.0 OD1 A:ASP68 3.4 61.0 1.0 C A:ASP68 3.6 55.1 1.0 CA A:LYS69 3.7 47.3 1.0 CA A:ASP68 3.8 54.4 1.0 CB A:LYS69 3.8 48.4 1.0 CB A:GLN70 3.9 76.8 1.0 CG A:GLN70 4.0 84.6 1.0 C A:LYS69 4.0 49.5 1.0 CA A:GLN70 4.2 63.8 1.0 O A:ALA67 4.4 46.8 1.0 CG A:ASP68 4.5 61.6 1.0 O A:ASP68 4.6 55.3 1.0 N A:ASP68 4.8 47.7 1.0 CB A:ASP68 4.8 58.6 1.0 C A:ALA67 4.9 49.8 1.0

Sodium binding site 5 out of 5 in the Crystal Structure of Rsgcamp in the Off State (Illuminated)


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 Rsgcamp in the Off State (Illuminated) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na509 b:37.3 occ:1.00 OG1 A:THR255 3.9 54.9 1.0 O A:TYR95 4.0 40.1 1.0 C A:TYR95 4.2 38.2 1.0 O A:GLU253 4.2 47.9 1.0 N A:THR255 4.3 43.6 1.0 N A:GLN96 4.4 37.3 1.0 N A:GLN97 4.4 44.6 1.0 CB A:TYR95 4.4 43.1 1.0 CB A:GLN97 4.4 63.3 1.0 C A:GLN96 4.5 38.6 1.0 CA A:ARG254 4.6 43.8 1.0 C A:ARG254 4.6 41.7 1.0 CA A:GLN96 4.6 37.3 1.0 C A:GLU253 4.6 45.7 1.0 CB A:THR255 4.8 47.5 1.0 N A:ARG254 4.8 44.6 1.0 CB A:GLU253 5.0 52.7 1.0 CA A:TYR95 5.0 41.0 1.0

J.P.Fuenzalida-Werner, K.Mishra, R.Janowski, D.Niessing, A.C.Stiel. Genetically Encoded Photo-Switchable Indicators, New Tools For Optoacoustic Imaging and Fluorescence Nanoscopy To Be Published.