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

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 5bye:

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

Chlorine (Cl) 1 atom

Sodium Binding Sites:

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 5bye

Go back to Sodium Binding Sites List in 5bye
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 5bye

Go back to Sodium Binding Sites List in 5bye
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

Reference:

J.Park, J.Chakrabarti, B.Singh, R.S.Gupta, M.S.Junop. Crystal Structure of Human Ribokinase in P212121 Spacegroup To Be Published.
Page generated: Tue Dec 15 10:29:56 2020

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