Sodium in PDB 6cym: Reversible Covalent Direct Thrombin Inhibitors

All present enzymatic activity of Reversible Covalent Direct Thrombin Inhibitors:
3.4.21.5;

The structure of Reversible Covalent Direct Thrombin Inhibitors, PDB code: 6cym was solved by M.Sivaraja, D.C.Williams, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.00 / 2.90
Space group	C 2 2 21
Cell size a, b, c (Å), α, β, γ (°)	91.670, 99.730, 146.010, 90.00, 90.00, 90.00
R / Rfree (%)	17.6 / 25.4

The binding sites of Sodium atom in the Reversible Covalent Direct Thrombin Inhibitors (pdb code 6cym). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Reversible Covalent Direct Thrombin Inhibitors, PDB code: 6cym:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Reversible Covalent Direct Thrombin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Reversible Covalent Direct Thrombin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ A:Na302 b:27.4 occ:1.00 O A:HOH405 2.6 33.8 1.0 O A:LYS250 2.7 45.1 1.0 O A:ARG247 2.9 58.3 1.0 O A:HOH406 2.9 35.0 1.0 O A:HOH401 3.2 32.4 1.0 O A:TYR204 3.4 51.5 1.0 C A:ARG247 3.8 61.6 1.0 C A:LYS250 3.9 45.7 1.0 OD1 A:ASP246 4.3 72.5 1.0 N A:LYS250 4.3 46.3 1.0 N A:ARG247 4.3 57.6 1.0 C A:ASP246 4.4 62.0 1.0 N A:GLY249 4.5 53.0 1.0 CA A:ASP248 4.5 59.6 1.0 CA A:ASP246 4.5 57.3 1.0 N A:ASP248 4.5 60.0 1.0 CD1 A:TYR251 4.6 45.0 1.0 C A:TYR204 4.6 48.8 1.0 CE1 A:TYR251 4.7 46.4 1.0 CA A:LYS250 4.7 44.4 1.0 O A:ASP246 4.8 63.5 1.0 CA A:ARG247 4.8 59.4 1.0 N A:TYR204 4.8 37.1 1.0 C A:ASP248 4.9 59.5 1.0 N A:TYR251 4.9 40.5 1.0

Sodium binding site 2 out of 2 in the Reversible Covalent Direct Thrombin Inhibitors


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Reversible Covalent Direct Thrombin Inhibitors within 5.0Å range: probe atom residue distance (Å) B Occ C:Na302 b:27.7 occ:1.00 O C:ARG247 2.4 50.5 1.0 O C:LYS250 2.6 49.4 1.0 C C:ARG247 3.4 49.3 1.0 N C:ARG247 3.7 49.0 1.0 C C:LYS250 3.8 48.4 1.0 C C:ASP246 3.9 56.6 1.0 O C:TYR204 4.0 37.7 1.0 CA C:ASP246 4.1 53.5 1.0 N C:LYS250 4.1 41.6 1.0 N C:ASP248 4.2 40.3 1.0 CA C:ARG247 4.2 46.6 1.0 OD1 C:ASP246 4.3 71.2 1.0 O C:ASP246 4.3 57.6 1.0 CA C:ASP248 4.4 38.6 1.0 N C:GLY249 4.4 47.5 1.0 CA C:LYS250 4.5 41.6 1.0 C C:ASP248 4.8 48.2 1.0 N C:TYR251 4.8 43.2 1.0 CB C:LYS250 4.8 43.2 1.0 CD1 C:TYR251 5.0 44.2 1.0 N C:ASP246 5.0 53.7 1.0

M.Sivaraja, N.Pozzi, M.Rienzo, K.Lin, T.P.Shiau, D.M.Clemens, L.Igoudin, P.Zalicki, S.S.Chang, M.A.Estiarte, K.M.Short, D.C.Williams, A.Datta, E.Di Cera, D.B.Kita. Reversible Covalent Direct Thrombin Inhibitors. Plos One V. 13 01377 2018.
ISSN: ESSN 1932-6203
PubMed: 30071045
DOI: 10.1371/JOURNAL.PONE.0201377