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Sodium in PDB 6z8x: X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3.

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3.

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3.:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3., PDB code: 6z8x was solved by R.Troisi, E.N.Timofeev, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.99 / 2.53
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 94.671, 94.671, 124.693, 90, 90, 120
R / Rfree (%) 24.5 / 29.2

Other elements in 6z8x:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3. also contains other interesting chemical elements:

Potassium (K) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3. (pdb code 6z8x). 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 A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3., PDB code: 6z8x:

Sodium binding site 1 out of 1 in 6z8x

Go back to Sodium Binding Sites List in 6z8x
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3.


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 A Thrombin Binding Aptamer Variant (Tba-3LEU), Which Contains Leucyl Amide in the Side Chain of THY3 at N3. within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:48.6
occ:1.00
 O H:LYS224 2.5 64.9 1.0
O H:ARG221 3.1 66.4 1.0
O H:TYR184A 3.3 84.5 1.0
O H:GLY188 3.6 58.4 1.0
C H:LYS224 3.8 66.4 1.0
OD1 H:ASP221A 3.8 64.2 1.0
N H:TYR184A 3.8 76.2 1.0
OD2 H:ASP189 3.9 62.2 1.0
N H:ARG221 4.0 63.5 1.0
CA H:ASP221A 4.1 62.5 1.0
C H:ARG221 4.1 64.7 1.0
C H:ASP221A 4.2 63.7 1.0
C H:TYR184A 4.3 81.1 1.0
CA H:TYR184A 4.4 78.0 1.0
CB H:ASP189 4.5 61.6 1.0
CA H:TYR225 4.6 67.8 1.0
CG H:ASP189 4.6 61.5 1.0
N H:TYR225 4.6 67.0 1.0
CB H:TYR184A 4.6 76.1 1.0
CD1 H:TYR225 4.7 67.3 1.0
CA H:ARG221 4.7 63.3 1.0
C H:GLY188 4.7 59.3 1.0
CA H:LYS224 4.7 66.8 1.0
N H:LYS224 4.7 67.1 1.0
CG H:ASP221A 4.8 62.9 1.0
C H:GLY184 4.9 75.6 1.0
CA H:GLY184 4.9 73.9 1.0
CB H:ASP221A 5.0 62.4 1.0
N H:ASP221A 5.0 61.7 1.0

Reference:

I.Smirnov, N.Kolganova, R.Troisi, F.Sica, E.Timofeev. Expanding the Recognition Interface of the Thrombin Binding Aptamer HD1 Through Modification of Residues T3 and T12 Mol.Ther. 2021.
ISSN: ESSN 1525-0024
DOI: 10.1016/J.OMTN.2021.01.004
Page generated: Tue Oct 8 15:24:36 2024

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