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

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 Beta

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 Beta:
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 Beta, PDB code: 7zkm 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) 59.10 / 2.00
Space group P 31 2 1
Cell size a, b, c (Å), α, β, γ (°) 76.6, 76.6, 129.38, 90, 90, 120
R / Rfree (%) 22.6 / 25.2

Other elements in 7zkm:

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 Beta also contains other interesting chemical elements:

Potassium (K) 2 atoms

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 Beta (pdb code 7zkm). 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 Beta, PDB code: 7zkm:

Sodium binding site 1 out of 1 in 7zkm

Go back to Sodium Binding Sites List in 7zkm
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 Beta


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 Beta within 5.0Å range:
probe atom residue distance (Å) B Occ
H:Na302

b:50.4
occ:1.00
 O H:ARG221 2.2 48.3 1.0
O H:LYS224 2.4 46.1 1.0
O H:HOH421 2.4 47.2 1.0
O H:HOH406 2.5 44.3 1.0
O H:HOH426 2.6 40.2 1.0
O H:HOH422 2.7 55.3 1.0
C H:ARG221 3.3 53.9 1.0
C H:LYS224 3.5 45.5 1.0
N H:LYS224 3.7 50.7 1.0
N H:ARG221 3.9 49.6 1.0
O H:TYR184A 4.0 52.3 1.0
N H:GLY223 4.1 54.1 1.0
N H:ASP222 4.1 55.4 1.0
C H:ASP221A 4.1 47.8 1.0
CA H:ASP222 4.1 57.2 1.0
CA H:LYS224 4.1 48.3 1.0
CA H:ARG221 4.2 53.9 1.0
C H:ASP222 4.4 56.5 1.0
CA H:ASP221A 4.4 46.8 1.0
O H:ASP221A 4.5 50.1 1.0
N H:TYR225 4.6 42.9 1.0
CB H:LYS224 4.6 50.1 1.0
OD1 H:ASP221A 4.7 52.1 1.0
C H:GLY223 4.7 52.6 1.0
O H:HOH419 4.7 58.0 1.0
CA H:TYR225 4.9 42.8 1.0
CD1 H:TYR225 4.9 45.6 1.0
CA H:GLY223 4.9 54.5 1.0
CE1 H:TYR225 5.0 48.4 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: Fri Apr 7 17:27:06 2023

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