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Potassium in PDB 9cva: Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp

Enzymatic activity of Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp

All present enzymatic activity of Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp:
2.7.1.15;

Protein crystallography data

The structure of Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp, PDB code: 9cva was solved by J.Park, N.Akanmori, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 55.76 / 1.60
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.38, 70.75, 90.65, 90, 92.36, 90
R / Rfree (%) 15.3 / 18.5

Other elements in 9cva:

The structure of Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms
Chlorine (Cl) 1 atom

Potassium Binding Sites:

The binding sites of Potassium atom in the Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp (pdb code 9cva). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp, PDB code: 9cva:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in 9cva

Go back to Potassium Binding Sites List in 9cva
Potassium binding site 1 out of 2 in the Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K404

b:29.7
occ:1.00
O A:GLY306 2.7 32.2 1.0
O A:ALA304 2.7 34.8 1.0
O A:ASP263 2.7 31.8 1.0
O A:SER301 2.8 30.8 1.0
O A:HOH602 2.8 29.4 1.0
OG A:SER310 2.9 27.7 1.0
O A:THR265 3.2 34.1 1.0
CB A:SER310 3.3 28.8 1.0
C A:SER301 3.7 30.7 1.0
C A:ASP263 3.8 34.9 1.0
C A:ALA304 3.9 37.4 1.0
C A:GLY306 3.9 34.6 1.0
CB A:ASP263 4.1 41.0 1.0
CA A:VAL302 4.2 31.6 1.0
CG A:ASP263 4.2 41.1 1.0
C A:THR265 4.3 31.7 1.0
N A:GLY306 4.3 36.8 1.0
N A:THR265 4.3 36.0 1.0
N A:VAL302 4.3 30.8 1.0
C A:ALA305 4.4 39.4 1.0
CA A:ASP263 4.5 40.0 1.0
OD1 A:ASP263 4.6 43.3 1.0
C A:THR264 4.6 34.6 1.0
C A:VAL302 4.6 34.6 1.0
OD2 A:ASP263 4.6 43.8 1.0
CA A:SER301 4.7 29.2 1.0
N A:ALA304 4.7 36.6 1.0
N A:THR264 4.7 36.4 1.0
CB A:SER301 4.7 27.3 1.0
CA A:GLY306 4.7 35.6 1.0
CA A:SER310 4.8 29.2 1.0
N A:ALA305 4.8 38.8 1.0
O A:ALA305 4.8 38.9 1.0
OG A:SER301 4.8 29.2 1.0
CA A:THR265 4.8 33.1 1.0
CA A:ALA304 4.8 38.8 1.0
CA A:THR264 4.8 35.7 1.0
O A:VAL302 4.8 35.5 1.0
CA A:ALA305 4.8 39.9 1.0
N A:THR307 4.9 32.9 1.0
O A:THR307 4.9 26.5 1.0
CA A:THR307 5.0 30.7 1.0

Potassium binding site 2 out of 2 in 9cva

Go back to Potassium Binding Sites List in 9cva
Potassium binding site 2 out of 2 in the Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K406

b:24.5
occ:1.00
O B:GLY306 2.6 27.5 1.0
O B:ASP263 2.7 25.2 1.0
O B:ALA304 2.7 25.8 1.0
O B:HOH610 2.8 25.4 1.0
O B:SER301 2.8 22.2 1.0
OG B:SER310 2.9 21.0 1.0
O B:THR265 3.2 27.6 1.0
CB B:SER310 3.3 23.6 1.0
C B:SER301 3.7 23.0 1.0
C B:ASP263 3.8 28.1 1.0
C B:GLY306 3.8 28.9 1.0
C B:ALA304 3.9 26.4 1.0
CB B:ASP263 4.1 30.8 1.0
CA B:VAL302 4.1 22.7 1.0
N B:GLY306 4.3 32.3 1.0
CG B:ASP263 4.3 33.8 1.0
C B:THR265 4.3 26.4 1.0
N B:VAL302 4.4 22.4 1.0
N B:THR265 4.4 27.8 1.0
C B:ALA305 4.5 31.2 1.0
CA B:ASP263 4.5 29.5 1.0
C B:VAL302 4.6 24.2 1.0
OD2 B:ASP263 4.6 34.3 1.0
C B:THR264 4.6 27.6 1.0
CA B:SER301 4.7 22.0 1.0
N B:ALA304 4.7 25.7 1.0
CA B:GLY306 4.7 30.3 1.0
CB B:SER301 4.7 21.8 1.0
N B:THR264 4.7 28.4 1.0
OG B:SER301 4.8 22.1 1.0
O B:VAL302 4.8 25.0 1.0
CA B:SER310 4.8 23.8 1.0
O B:ALA305 4.8 31.1 1.0
N B:ALA305 4.8 27.1 1.0
CA B:ALA304 4.8 25.8 1.0
N B:THR307 4.8 26.3 1.0
OD1 B:ASP263 4.8 34.7 1.0
CA B:ALA305 4.8 29.7 1.0
CA B:THR264 4.9 27.6 1.0
O B:THR307 4.9 23.0 1.0
CA B:THR265 4.9 28.8 1.0
CA B:THR307 4.9 25.7 1.0

Reference:

N.N.Akanmori, J.Park. Crystal Structure of Human Ribokinase in Complex with K+, MG2+, and Ampcp To Be Published.
Page generated: Sat Aug 23 04:00:52 2025

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