Sodium in PDB 9c50: Replacement of A Single Residue Changes the Primary Specificity of Thrombin

The structure of Replacement of A Single Residue Changes the Primary Specificity of Thrombin, PDB code: 9c50 was solved by A.Dei Rossi, S.Deavila, B.M.Mohammed, S.Korolev, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.85 / 2.50
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	131.15, 76.732, 89.588, 90, 113.77, 90
R / Rfree (%)	19 / 24.5

The binding sites of Sodium atom in the Replacement of A Single Residue Changes the Primary Specificity of Thrombin (pdb code 9c50). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Replacement of A Single Residue Changes the Primary Specificity of Thrombin, PDB code: 9c50:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Replacement of A Single Residue Changes the Primary Specificity of Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Replacement of A Single Residue Changes the Primary Specificity of Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na301 b:41.2 occ:1.00 O B:LYS224 2.3 36.1 1.0 O B:ARG221A 2.3 40.8 1.0 O B:HOH427 2.4 50.0 1.0 O B:HOH423 2.6 36.7 1.0 O B:HOH421 2.6 34.8 1.0 O B:HOH413 3.1 40.8 1.0 C B:LYS224 3.3 35.8 1.0 C B:ARG221A 3.4 39.9 1.0 O B:HOH439 3.7 35.3 1.0 N B:LYS224 3.8 36.0 1.0 N B:ARG221A 3.9 36.9 1.0 CA B:LYS224 4.0 35.8 1.0 C B:ASP221 4.0 35.2 1.0 O B:HOH406 4.1 50.0 1.0 O B:TYR184A 4.1 36.6 1.0 CA B:ARG221A 4.3 37.8 1.0 N B:ASP222 4.3 41.0 1.0 CA B:ASP221 4.3 39.6 1.0 N B:TYR225 4.3 36.5 1.0 N B:GLY223 4.3 39.7 1.0 CA B:ASP222 4.3 43.1 1.0 CB B:LYS224 4.4 38.3 1.0 O B:HOH412 4.4 35.2 1.0 C B:ASP222 4.5 40.3 1.0 O B:ASP221 4.6 37.0 1.0 CA B:TYR225 4.6 35.8 1.0 C B:GLY223 4.7 36.0 1.0 OD1 B:ASP221 4.8 38.2 1.0 N B:ASP221 4.9 37.7 1.0

Sodium binding site 2 out of 2 in the Replacement of A Single Residue Changes the Primary Specificity of Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Replacement of A Single Residue Changes the Primary Specificity of Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ D:Na301 b:50.0 occ:1.00 O D:HOH451 2.3 35.7 1.0 O D:LYS224 2.3 35.8 1.0 O D:HOH406 2.3 50.0 1.0 O D:ARG221A 2.3 41.9 1.0 O D:HOH416 2.8 37.5 1.0 C D:LYS224 3.2 38.9 1.0 C D:ARG221A 3.3 40.0 1.0 O D:HOH423 3.4 36.7 1.0 N D:ARG221A 3.6 37.5 1.0 O D:HOH446 3.7 31.3 1.0 C D:ASP221 3.8 40.3 1.0 N D:LYS224 3.9 38.0 1.0 CA D:ASP221 3.9 35.7 1.0 CA D:LYS224 3.9 42.5 1.0 CA D:ARG221A 4.1 33.9 1.0 N D:TYR225 4.1 37.7 1.0 CB D:LYS224 4.1 43.1 1.0 O D:HOH410 4.3 37.0 1.0 N D:ASP222 4.3 36.6 1.0 CA D:TYR225 4.4 39.2 1.0 O D:ASP221 4.4 37.4 1.0 O D:HOH441 4.5 33.3 1.0 N D:ASP221 4.5 38.5 1.0 OD1 D:ASP221 4.5 32.6 1.0 CA D:ASP222 4.6 40.7 1.0 N D:GLY223 4.6 32.6 1.0 O D:TYR184A 4.6 40.1 1.0 O D:HOH432 4.7 32.1 1.0 C D:ASP222 4.7 40.8 1.0 CD1 D:TYR225 4.8 38.6 1.0 OD2 D:ASP189 4.8 29.7 1.0 C D:GLY223 4.9 42.9 1.0 CB D:ARG221A 4.9 35.8 1.0

A.D.Rossi, S.Deavila, B.M.Mohammed, S.Korolev, E.Di Cera. Replacement of A Single Residue Changes the Primary Specificity of Thrombin. J.Thromb.Haemost. 2025.
ISSN: ESSN 1538-7836
PubMed: 39756655
DOI: 10.1016/J.JTHA.2024.12.024