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Sodium in PDB 7zko: X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta

Enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta

All present enzymatic activity of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta:
3.4.21.5;

Protein crystallography data

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta, PDB code: 7zko was solved by R.Troisi, F.Sica, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 49.02 / 2.50
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 75.87, 75.87, 146.9, 90, 90, 120
R / Rfree (%) 24.6 / 29.5

Other elements in 7zko:

The structure of X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta 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 Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta (pdb code 7zko). 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 Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta, PDB code: 7zko:

Sodium binding site 1 out of 1 in 7zko

Go back to Sodium Binding Sites List in 7zko
Sodium binding site 1 out of 1 in the X-Ray Structure of the Complex Between Human Alpha Thrombin and A Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta


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 Pseudo-Cyclic Thrombin Binding Aptamer (Tba-Nnp/Ddp) - Crystal Form Delta within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:79.1
occ:1.00
 O H:HOH409 2.2 70.6 1.0
O H:HOH401 2.4 58.4 1.0
O H:LYS224 2.8 90.5 1.0
O H:ARG221 2.9 84.7 1.0
O H:TYR184A 3.5 85.3 1.0
C H:ARG221 3.6 86.8 1.0
C H:LYS224 4.0 87.5 1.0
N H:ARG221 4.1 75.7 1.0
N H:ASP222 4.2 89.1 1.0
CA H:ASP222 4.2 87.1 1.0
N H:LYS224 4.5 87.1 1.0
N H:GLY223 4.5 86.3 1.0
CA H:ARG221 4.5 82.6 1.0
C H:ASP221A 4.6 84.8 1.0
CD1 H:TYR225 4.7 99.3 1.0
OD1 H:ASP221A 4.7 76.0 1.0
C H:TYR184A 4.7 81.6 1.0
CA H:ASP221A 4.7 82.2 1.0
CE1 H:TYR225 4.7 100.2 1.0
C H:ASP222 4.8 86.1 1.0
CA H:LYS224 4.8 88.3 1.0
OD1 H:ASP222 4.9 95.2 1.0
N H:TYR184A 5.0 73.2 1.0
N H:TYR225 5.0 82.3 1.0

Reference:

R.Troisi, C.Riccardi, K.Perez De Carvasal, M.Smietana, F.Morvan, P.Del Vecchio, D.Montesarchio, F.Sica. A Terminal Functionalization Strategy Reveals Unusual Binding Abilities of Anti-Thrombin Anticoagulant Aptamers. Mol Ther Nucleic Acids V. 30 585 2022.
ISSN: ISSN 2162-2531
PubMed: 36457701
DOI: 10.1016/J.OMTN.2022.11.007
Page generated: Wed Oct 9 10:17:18 2024

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