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Sodium in PDB 4dii: X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions, PDB code: 4dii was solved by I.Russo Krauss, A.Merlino, L.Mazzarella, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 50.00 / 2.05
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 43.369, 45.299, 51.519, 68.97, 86.11, 69.66
R / Rfree (%) 17.4 / 22.6

Other elements in 4dii:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions also contains other interesting chemical elements:

Potassium (K) 1 atom
Zinc (Zn) 2 atoms
Chlorine (Cl) 2 atoms

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions (pdb code 4dii). 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 X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions, PDB code: 4dii:

Sodium binding site 1 out of 1 in 4dii

Go back to Sodium Binding Sites List in 4dii
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of X-Ray Structure of the Complex Between Human Alpha Thrombin and Thrombin Binding Aptamer in the Presence of Potassium Ions within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na303

b:49.4
occ:1.00
O H:ARG221 2.5 25.4 1.0
O H:HOH418 2.5 35.3 1.0
O H:HOH464 2.6 25.0 1.0
O H:LYS224 2.7 27.0 1.0
O H:HOH468 3.4 43.0 1.0
O H:HOH453 3.4 33.6 1.0
O H:HOH448 3.4 32.8 1.0
C H:ARG221 3.5 27.0 1.0
C H:LYS224 3.6 27.0 1.0
N H:ARG221 3.6 24.7 1.0
C H:ASP221A 3.7 25.2 1.0
CA H:ASP221A 3.9 25.5 1.0
N H:LYS224 4.1 28.1 1.0
CA H:ARG221 4.2 26.7 1.0
O H:ASP221A 4.2 24.2 1.0
OD1 H:ASP221A 4.3 31.3 1.0
CA H:LYS224 4.3 27.3 1.0
O H:HOH431 4.4 24.8 1.0
CB H:LYS224 4.4 28.2 1.0
N H:TYR225 4.5 25.6 1.0
N H:ASP222 4.6 26.9 1.0
O H:TYR184A 4.6 29.3 1.0
CA H:TYR225 4.7 24.7 1.0
N H:ASP221A 4.7 23.8 1.0
N H:GLY223 4.8 26.9 1.0
OD2 H:ASP189 4.8 25.0 1.0
O H:HOH413 4.9 26.9 1.0
CA H:ASP222 4.9 27.5 1.0
O H:GLY188 4.9 24.1 1.0

Reference:

I.Russo Krauss, A.Merlino, A.Randazzo, E.Novellino, L.Mazzarella, F.Sica. High-Resolution Structures of Two Complexes Between Thrombin and Thrombin-Binding Aptamer Shed Light on the Role of Cations in the Aptamer Inhibitory Activity. Nucleic Acids Res. V. 40 8119 2012.
ISSN: ISSN 0305-1048
PubMed: 22669903
DOI: 10.1093/NAR/GKS512
Page generated: Tue Dec 15 06:36:54 2020

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