Sodium in PDB 5byc: Crystal Structure of Human Ribokinase in C2 Spacegroup

All present enzymatic activity of Crystal Structure of Human Ribokinase in C2 Spacegroup:
2.7.1.15;

The structure of Crystal Structure of Human Ribokinase in C2 Spacegroup, PDB code: 5byc was solved by J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	45.49 / 1.95
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	180.920, 47.040, 80.910, 90.00, 98.73, 90.00
R / Rfree (%)	17.3 / 22

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in C2 Spacegroup (pdb code 5byc). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Ribokinase in C2 Spacegroup, PDB code: 5byc:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Ribokinase in C2 Spacegroup


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 Human Ribokinase in C2 Spacegroup within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:24.0 occ:1.00 O A:SER301 2.3 21.9 1.0 O A:HOH620 2.4 22.6 1.0 O A:ALA304 2.4 25.9 1.0 O A:HOH563 2.4 24.1 1.0 O A:ASP263 2.5 28.3 1.0 OG A:SER310 2.8 19.6 1.0 C A:SER301 3.3 21.0 1.0 CB A:SER310 3.3 21.0 1.0 C A:ASP263 3.6 31.1 1.0 C A:ALA304 3.6 29.1 1.0 CA A:VAL302 3.8 24.8 1.0 O A:THR265 3.9 23.3 1.0 N A:VAL302 3.9 22.0 1.0 C A:VAL302 4.2 27.8 1.0 CB A:ASP263 4.3 39.6 1.0 N A:ALA304 4.3 29.7 1.0 CA A:SER301 4.3 18.6 1.0 CG A:ASP263 4.3 41.8 1.0 CA A:ASP263 4.4 35.9 1.0 O A:VAL302 4.5 28.5 1.0 CB A:SER301 4.5 17.1 1.0 N A:THR264 4.5 30.1 1.0 OD2 A:ASP263 4.5 49.9 1.0 N A:ALA305 4.5 30.3 1.0 OG A:SER301 4.5 17.0 1.0 CA A:ALA305 4.6 30.3 1.0 CA A:ALA304 4.6 30.7 1.0 C A:ALA305 4.6 28.4 1.0 CA A:THR264 4.6 27.7 1.0 N A:THR265 4.7 26.4 1.0 N A:THR307 4.7 23.6 1.0 C A:THR264 4.7 26.0 1.0 OD1 A:ASP263 4.7 42.0 1.0 N A:ASP263 4.8 35.2 1.0 CA A:SER310 4.8 21.3 1.0 N A:GLN303 4.8 28.8 1.0 N A:GLY306 4.9 28.1 1.0 O A:ALA305 4.9 26.4 1.0 C A:THR265 4.9 23.3 1.0 O A:THR307 4.9 17.8 1.0 CB A:VAL302 4.9 25.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Ribokinase in C2 Spacegroup


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 Human Ribokinase in C2 Spacegroup within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:24.6 occ:1.00 O B:HOH608 2.3 25.9 1.0 O B:ASP263 2.4 27.3 1.0 O B:HOH612 2.4 21.1 1.0 O B:SER301 2.4 22.9 1.0 O B:ALA304 2.5 25.5 1.0 OG B:SER310 2.8 19.3 1.0 CB B:SER310 3.3 20.8 1.0 C B:SER301 3.3 20.8 1.0 C B:ASP263 3.5 30.0 1.0 C B:ALA304 3.7 28.0 1.0 CA B:VAL302 3.8 24.5 1.0 O B:THR265 3.8 26.6 1.0 N B:VAL302 3.9 22.5 1.0 CB B:ASP263 4.2 35.1 1.0 C B:VAL302 4.3 26.1 1.0 CG B:ASP263 4.3 35.6 1.0 CA B:SER301 4.4 20.3 1.0 CA B:ASP263 4.4 33.4 1.0 N B:ALA304 4.4 28.1 1.0 N B:THR264 4.4 28.8 1.0 O B:VAL302 4.5 28.4 1.0 CB B:SER301 4.5 18.9 1.0 OD2 B:ASP263 4.5 38.7 1.0 OG B:SER301 4.5 19.2 1.0 N B:THR265 4.5 26.5 1.0 CA B:THR264 4.6 26.6 1.0 CA B:ALA305 4.6 30.6 1.0 N B:ALA305 4.6 29.9 1.0 CA B:ALA304 4.6 29.2 1.0 C B:THR264 4.6 25.8 1.0 C B:ALA305 4.7 29.1 1.0 N B:ASP263 4.7 33.3 1.0 N B:THR307 4.7 26.3 1.0 OD1 B:ASP263 4.7 35.4 1.0 CA B:SER310 4.8 21.2 1.0 N B:GLY306 4.9 28.9 1.0 O B:THR307 4.9 20.2 1.0 C B:THR265 4.9 25.6 1.0 N B:GLN303 4.9 25.8 1.0 O B:ALA305 5.0 26.9 1.0 CB B:VAL302 5.0 25.9 1.0

J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop. Crystal Structure of Unliganded Human Ribokinase in C2 Spacegroup To Be Published.