Sodium in PDB 8tqs: Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker.

The structure of Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker., PDB code: 8tqs was solved by S.Krishnaswamy, S.Kumar, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.14 / 2.21
Space group	P 41 21 2
Cell size a, b, c (Å), α, β, γ (°)	81.626, 81.626, 190.514, 90, 90, 90
R / Rfree (%)	21.4 / 24.5

The structure of Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker. also contains other interesting chemical elements:

Magnesium

(Mg)

1 atom

The binding sites of Sodium atom in the Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker. (pdb code 8tqs). 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 Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker., PDB code: 8tqs:

Sodium binding site 1 out of 1 in the Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker. within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:85.5 occ:1.00 O H:LYS224 2.3 75.9 1.0 O H:HOH402 2.4 66.8 1.0 O H:HOH404 2.5 75.1 1.0 O H:ARG221A 2.9 87.1 1.0 C H:LYS224 3.3 79.4 1.0 CA H:ASP221 3.9 85.3 1.0 C H:ARG221A 3.9 85.6 1.0 N H:ARG221A 4.0 80.9 1.0 C H:ASP221 4.0 82.7 1.0 N H:TYR225 4.2 76.8 1.0 CA H:TYR225 4.2 71.0 1.0 CA H:LYS224 4.3 81.2 1.0 N H:LYS224 4.4 85.0 1.0 N H:ASP221 4.5 84.5 1.0 O H:TYR184A 4.5 75.0 1.0 OD2 H:ASP189 4.5 79.3 1.0 OD1 H:ASP221 4.5 87.9 1.0 CB H:LYS224 4.5 85.2 1.0 O H:ASP221 4.6 89.4 1.0 CA H:ARG221A 4.6 81.6 1.0 CD1 H:TYR225 4.7 72.0 1.0 O H:GLY188 4.9 76.3 1.0 N H:ASP222 4.9 89.2 1.0 CG H:ASP189 5.0 82.0 1.0

S.Krishnaswamy, S.Kumar. Complex of Human Thrombin (S195A) Bound to A Bivalent Inhibitor Comprised of Dna Aptamer HD22 Conjugated to Dabigatran with A Linker. Nat Commun 2024.
ISSN: ESSN 2041-1723