Sodium in PDB 6y9h: Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2):
3.4.21.5;

The structure of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2), PDB code: 6y9h was solved by A.Sandner, A.Heine, G.Klebe, N.Abazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.64 / 1.48
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.333, 71.29, 72.534, 90, 100.5, 90
R / Rfree (%)	13.8 / 17

The structure of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) also contains other interesting chemical elements:

Fluorine

(F)

6 atoms

The binding sites of Sodium atom in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) (pdb code 6y9h). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2), PDB code: 6y9h:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:13.5 occ:1.00 O H:THR172 2.3 12.5 1.0 O H:LYS169 2.4 13.9 1.0 O H:HOH585 2.4 28.3 1.0 O H:HOH504 2.7 21.2 1.0 HA H:ASP170 3.3 15.3 1.0 HG2 H:LYS169 3.5 24.4 1.0 C H:LYS169 3.5 13.5 1.0 H H:THR172 3.5 15.5 1.0 C H:THR172 3.5 12.6 1.0 HA H:ARG173 3.6 15.9 1.0 HG3 H:LYS169 4.0 24.4 1.0 CA H:ASP170 4.0 12.7 1.0 N H:ASP170 4.2 13.2 1.0 CG H:LYS169 4.2 20.3 1.0 N H:THR172 4.3 12.9 1.0 CA H:ARG173 4.4 13.3 1.0 N H:ARG173 4.4 13.0 1.0 C H:ASP170 4.4 12.7 1.0 HG23 H:THR172 4.4 16.4 1.0 HA H:LYS169 4.5 15.4 1.0 O H:HOH440 4.5 36.5 1.0 CA H:THR172 4.5 12.8 1.0 CA H:LYS169 4.5 12.8 1.0 HG22 H:THR172 4.6 16.4 1.0 OD1 H:ASP170 4.8 16.7 1.0 O H:ASP170 4.8 12.7 1.0 HE2 H:LYS169 4.8 31.7 1.0 N H:SER171 4.9 12.8 1.0 HE3 H:LYS169 4.9 31.7 1.0 H H:SER171 4.9 15.3 1.0 CB H:LYS169 4.9 15.4 1.0 CG2 H:THR172 4.9 13.6 1.0 C H:ARG173 5.0 14.0 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:17.9 occ:1.00 O H:HOH486 2.3 19.1 1.0 O H:ARG221A 2.3 19.1 1.0 O H:HOH567 2.4 18.3 1.0 O H:LYS224 2.4 14.6 1.0 O H:HOH492 2.5 14.8 1.0 O H:HOH485 2.7 19.3 1.0 H H:LYS224 3.3 19.5 1.0 C H:ARG221A 3.4 19.4 1.0 C H:LYS224 3.5 13.9 1.0 HA H:ASP221 3.7 22.9 1.0 HA H:ASP222 3.8 25.4 1.0 O H:HOH506 3.9 15.6 1.0 N H:ARG221A 3.9 20.1 1.0 N H:LYS224 3.9 16.2 1.0 H H:ARG221A 3.9 24.2 1.0 HB2 H:LYS224 3.9 19.0 1.0 O H:HOH516 4.0 21.1 1.0 H H:GLY223 4.0 23.4 1.0 HA H:TYR225 4.1 14.8 1.0 O H:TYR184A 4.1 17.4 1.0 C H:ASP221 4.1 20.6 1.0 CA H:LYS224 4.2 14.4 1.0 O H:HOH500 4.2 16.2 1.0 N H:ASP222 4.2 20.1 1.0 CA H:ARG221A 4.2 19.6 1.0 N H:GLY223 4.3 19.5 1.0 CA H:ASP222 4.3 21.1 1.0 CA H:ASP221 4.4 19.1 1.0 N H:TYR225 4.5 13.7 1.0 C H:ASP222 4.5 20.7 1.0 CB H:LYS224 4.6 15.8 1.0 O H:ASP221 4.6 22.3 1.0 OD1 H:ASP221 4.7 19.0 1.0 CA H:TYR225 4.8 12.3 1.0 HB2 H:ARG221A 4.8 25.9 1.0 C H:GLY223 4.9 16.6 1.0 HA3 H:GLY184 4.9 16.0 1.0 O H:HOH563 4.9 22.4 1.0 HA H:ARG221A 4.9 23.6 1.0 H H:ASP221 5.0 21.9 1.0 H H:ASP222 5.0 24.2 1.0 HB2 H:ASP189 5.0 17.9 1.0

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-M-Trifluoromethylbenzylamide Derivative (PHE2) To Be Published.