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Sodium in PDB 5eyn: Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form

Enzymatic activity of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form

All present enzymatic activity of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form:
2.7.1.4;

Protein crystallography data

The structure of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form, PDB code: 5eyn was solved by R.Paul, S.Nath, U.Sen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 32.15 / 1.29
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 64.300, 107.218, 41.618, 90.00, 90.00, 90.00
R / Rfree (%) 14.1 / 16.9

Other elements in 5eyn:

The structure of Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form also contains other interesting chemical elements:

Fluorine (F) 3 atoms
Calcium (Ca) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form (pdb code 5eyn). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form, PDB code: 5eyn:

Sodium binding site 1 out of 1 in 5eyn

Go back to Sodium Binding Sites List in 5eyn
Sodium binding site 1 out of 1 in the Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form


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 Fructokinase From Vibrio Cholerae O395 in Fructose, Adp, Beryllium Trifluoride and Calcium Ion Bound Form within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na405

b:16.4
occ:1.00
 O A:HOH609 2.0 12.0 1.0
O A:GLY307 2.1 11.2 1.0
O A:GLN305 2.2 11.2 1.0
O A:HOH655 2.4 15.0 1.0
O A:ALA302 2.5 12.5 1.0
C A:GLY307 3.2 10.0 1.0
C A:GLN305 3.4 10.5 1.0
H A:GLN305 3.5 13.7 1.0
H A:ALA311 3.6 12.3 1.0
HA A:ALA308 3.7 10.9 1.0
C A:ALA302 3.7 11.2 1.0
HB A:THR310 3.8 12.8 1.0
HB3 A:ASP260 3.8 13.8 1.0
HB3 A:ALA311 3.8 16.1 1.0
N A:GLY307 3.9 10.1 1.0
H A:THR310 4.0 10.6 1.0
C A:LYS306 4.0 10.5 1.0
H A:GLY307 4.0 12.2 1.0
HA A:THR303 4.0 14.2 1.0
N A:ALA308 4.1 8.6 1.0
HB2 A:GLN305 4.1 15.4 1.0
CA A:ALA308 4.2 9.1 1.0
CA A:GLY307 4.2 9.9 1.0
C A:ALA308 4.2 9.6 1.0
HA A:LYS306 4.2 12.9 1.0
O A:ALA308 4.2 10.1 1.0
N A:GLN305 4.2 11.4 1.0
HB1 A:ALA302 4.2 13.4 1.0
O A:ASP260 4.3 11.3 1.0
O A:LYS306 4.3 11.4 1.0
N A:LYS306 4.3 10.4 1.0
CA A:GLN305 4.3 10.9 1.0
O A:THR262 4.3 12.3 1.0
HA A:ALA302 4.4 12.8 1.0
N A:ALA311 4.4 10.2 1.0
CA A:LYS306 4.4 10.8 1.0
OD2 A:ASP260 4.5 14.2 1.0
N A:THR310 4.5 8.8 1.0
HA3 A:GLY307 4.6 11.9 1.0
CA A:ALA302 4.6 10.7 1.0
CB A:ALA311 4.6 13.4 1.0
HB2 A:ALA311 4.6 16.1 1.0
N A:THR303 4.6 11.1 1.0
CB A:THR310 4.7 10.6 1.0
CA A:THR303 4.7 11.9 1.0
CB A:GLN305 4.7 12.8 1.0
CB A:ASP260 4.7 11.5 1.0
N A:MET309 4.8 8.9 1.0
C A:THR303 4.8 11.2 1.0
CG A:ASP260 4.9 12.7 1.0
H A:ALA308 4.9 10.3 1.0
CB A:ALA302 4.9 11.2 1.0
HA2 A:GLY307 4.9 11.9 1.0
H A:THR304 4.9 13.9 1.0
OG1 A:THR310 4.9 10.4 1.0
HB3 A:GLN305 4.9 15.4 1.0
HB A:THR262 5.0 12.2 1.0

Reference:

R.Paul, S.Nath, U.Sen. Crystal Structure of Fructokinase From Vibrio Cholerae O395 in Apo Form To Be Published.
Page generated: Mon Oct 7 20:54:33 2024

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