Sodium in PDB 5bye: Crystal Structure of Human Ribokinase in P212121 Spacegroup

All present enzymatic activity of Crystal Structure of Human Ribokinase in P212121 Spacegroup:
2.7.1.15;

The structure of Crystal Structure of Human Ribokinase in P212121 Spacegroup, PDB code: 5bye 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)	47.74 / 1.75
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	56.250, 65.480, 180.560, 90.00, 90.00, 90.00
R / Rfree (%)	19 / 22.9

The structure of Crystal Structure of Human Ribokinase in P212121 Spacegroup also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Crystal Structure of Human Ribokinase in P212121 Spacegroup (pdb code 5bye). 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 P212121 Spacegroup, PDB code: 5bye:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Ribokinase in P212121 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 P212121 Spacegroup within 5.0Å range: probe atom residue distance (Å) B Occ A:Na401 b:27.2 occ:1.00 O A:SER301 2.2 30.4 1.0 O A:ALA304 2.3 31.9 1.0 O A:HOH622 2.3 32.0 1.0 O A:ASP263 2.4 33.7 1.0 O A:HOH602 2.4 30.6 1.0 OG A:SER310 3.0 25.8 1.0 C A:SER301 3.2 30.2 1.0 CB A:SER310 3.4 28.6 1.0 C A:ALA304 3.5 37.0 1.0 C A:ASP263 3.6 37.1 1.0 CA A:VAL302 3.7 32.2 1.0 N A:VAL302 3.8 29.4 1.0 O A:THR265 3.9 31.3 1.0 C A:VAL302 4.0 34.9 1.0 O A:VAL302 4.2 38.3 1.0 N A:ALA304 4.2 35.6 1.0 OD2 A:ASP263 4.2 42.5 1.0 CB A:ASP263 4.3 40.9 1.0 CA A:SER301 4.3 28.2 1.0 N A:ALA305 4.4 38.8 1.0 CA A:ALA305 4.4 38.9 1.0 CA A:ASP263 4.4 39.4 1.0 CG A:ASP263 4.4 43.9 1.0 CA A:ALA304 4.5 36.3 1.0 OG A:SER301 4.5 28.7 1.0 N A:THR264 4.5 36.9 1.0 C A:ALA305 4.6 37.8 1.0 CB A:SER301 4.6 27.2 1.0 CA A:THR264 4.6 35.2 1.0 C A:THR264 4.7 33.5 1.0 N A:THR265 4.7 34.7 1.0 N A:GLN303 4.8 34.5 1.0 N A:ASP263 4.8 40.7 1.0 N A:GLY306 4.8 36.6 1.0 N A:THR307 4.8 30.7 1.0 C A:THR265 4.9 30.8 1.0 CA A:SER310 4.9 29.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Ribokinase in P212121 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 P212121 Spacegroup within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:45.6 occ:1.00 O B:SER301 2.4 49.1 1.0 O B:GLY306 2.4 48.5 1.0 O B:ALA304 2.5 57.3 1.0 OG B:SER310 2.9 45.3 1.0 CB B:SER310 3.3 47.7 1.0 C B:SER301 3.4 49.6 1.0 C B:GLY306 3.7 49.5 1.0 C B:ALA304 3.8 58.9 1.0 CA B:VAL302 3.9 58.0 1.0 N B:VAL302 4.0 52.8 1.0 O B:VAL302 4.1 65.8 1.0 C B:VAL302 4.1 60.4 1.0 N B:ALA304 4.3 59.9 1.0 N B:GLY306 4.3 56.3 1.0 C B:ALA305 4.4 56.2 1.0 CA B:SER301 4.5 48.9 1.0 CA B:ALA304 4.6 59.9 1.0 N B:THR307 4.6 44.7 1.0 CA B:GLY306 4.6 51.8 1.0 O B:ALA305 4.7 54.4 1.0 N B:ALA305 4.7 60.0 1.0 CA B:ALA305 4.8 59.6 1.0 O B:THR307 4.8 37.8 1.0 CA B:SER310 4.8 45.8 1.0 OG B:SER301 4.8 52.6 1.0 CA B:THR307 4.8 42.5 1.0 CB B:SER301 4.8 47.5 1.0 N B:GLN303 4.9 62.7 1.0

J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop. Crystal Structure of Human Ribokinase in P212121 Spacegroup To Be Published.