Sodium in PDB 8j98: A Near-Infrared Fluorescent Protein of De Novo Backbone Design

The structure of A Near-Infrared Fluorescent Protein of De Novo Backbone Design, PDB code: 8j98 was solved by X.Hu, Y.Xu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	34.69 / 2.90
Space group	P 65
Cell size a, b, c (Å), α, β, γ (°)	105.987, 105.987, 41.691, 90, 90, 120
R / Rfree (%)	20.9 / 24.6

The binding sites of Sodium atom in the A Near-Infrared Fluorescent Protein of De Novo Backbone Design (pdb code 8j98). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the A Near-Infrared Fluorescent Protein of De Novo Backbone Design, PDB code: 8j98:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the A Near-Infrared Fluorescent Protein of De Novo Backbone Design


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of A Near-Infrared Fluorescent Protein of De Novo Backbone Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Na301 b:20.5 occ:1.00 CG1 A:VAL168 3.4 24.0 1.0 N A:ILE117 3.7 30.0 1.0 CA A:GLY116 3.7 26.2 1.0 O A:GLU110 3.7 34.7 1.0 CD1 A:ILE117 4.0 32.9 1.0 CD2 A:LEU111 4.0 16.4 1.0 CG A:GLU110 4.2 31.3 1.0 CA A:LEU111 4.2 22.9 1.0 C A:GLY116 4.2 31.0 1.0 C A:GLU110 4.2 30.4 1.0 N A:LEU111 4.4 26.6 1.0 CB A:ILE117 4.5 26.0 1.0 CG1 A:ILE117 4.7 36.1 1.0 CA A:ILE117 4.7 28.6 1.0 O A:GLY115 4.8 29.5 1.0 CB A:VAL168 4.8 33.9 1.0 CB A:GLU110 4.8 30.0 1.0 CG A:LEU111 4.9 20.3 1.0 N A:GLY116 4.9 27.7 1.0

Sodium binding site 2 out of 2 in the A Near-Infrared Fluorescent Protein of De Novo Backbone Design


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of A Near-Infrared Fluorescent Protein of De Novo Backbone Design within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:33.4 occ:1.00 N A:SER120 3.1 25.6 1.0 O A:GLY116 3.1 30.2 1.0 OD2 A:ASP123 3.1 29.7 1.0 CB A:PHE119 3.5 24.5 1.0 CB A:SER120 3.6 20.1 1.0 N A:PHE119 3.7 25.5 1.0 CA A:PHE119 3.9 26.5 1.0 CA A:SER120 3.9 23.1 1.0 C A:PHE119 3.9 20.8 1.0 CD2 A:PHE119 3.9 23.7 1.0 O A:ILE117 4.1 36.9 1.0 CG A:ASP123 4.2 31.4 1.0 CG A:PHE119 4.2 26.9 1.0 C A:GLY116 4.2 31.0 1.0 C A:ILE117 4.3 33.4 1.0 CB A:ASP123 4.6 29.8 1.0 C A:ALA118 4.7 28.8 1.0 CA A:ILE117 4.7 28.6 1.0 N A:ALA118 4.8 26.2 1.0 OG A:SER120 4.9 26.8 1.0 N A:ILE117 5.0 30.0 1.0

X.Hu, Y.Xu. De Novo Backbone Design For Monomerization of Near-Infrared Fluorescent Protein To Be Published.