Sodium in PDB 6yhj: Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E):
3.4.21.5;

The structure of Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E), PDB code: 6yhj was solved by A.Sandner, A.Heine, G.Klebe, C.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.53 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.285, 71.399, 72.56, 90, 100.58, 90
R / Rfree (%)	12.7 / 15.4

The structure of Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E) also contains other interesting chemical elements:

Chlorine

(Cl)

2 atoms

The binding sites of Sodium atom in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E) (pdb code 6yhj). 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-2-Chlorothiophen Derivative (16E), PDB code: 6yhj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)


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-2-Chlorothiophen Derivative (16E) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:18.4 occ:1.00 O H:HOH579 2.3 20.9 1.0 O H:ARG221A 2.3 20.4 1.0 O H:LYS224 2.4 15.1 0.4 O H:LYS224 2.4 15.0 0.6 O H:HOH478 2.4 18.6 1.0 O H:HOH471 2.5 16.5 1.0 O H:HOH485 2.8 23.2 1.0 H H:LYS224 3.2 20.7 0.4 H H:LYS224 3.3 20.8 0.6 C H:ARG221A 3.4 20.5 1.0 C H:LYS224 3.4 15.1 0.4 C H:LYS224 3.4 15.0 0.6 HA H:ASP221 3.7 23.5 1.0 HA H:ASP222 3.8 27.9 1.0 HB2 H:LYS224 3.8 20.9 0.6 O H:HOH529 3.8 17.4 1.0 HB2 H:LYS224 3.8 20.3 0.4 N H:LYS224 3.9 17.2 0.4 N H:ARG221A 3.9 20.6 1.0 N H:LYS224 3.9 17.3 0.6 H H:ARG221A 3.9 24.8 1.0 H H:GLY223 4.0 26.1 1.0 HA H:TYR225 4.0 16.2 1.0 O H:HOH464 4.0 23.7 1.0 C H:ASP221 4.1 20.4 1.0 O H:TYR184A 4.1 18.9 1.0 CA H:LYS224 4.1 16.8 0.6 CA H:LYS224 4.1 16.5 0.4 N H:ASP222 4.2 21.9 1.0 CA H:ARG221A 4.2 21.0 1.0 O H:HOH495 4.3 17.5 1.0 N H:GLY223 4.3 21.8 1.0 CA H:ASP222 4.3 23.3 1.0 CA H:ASP221 4.4 19.6 1.0 N H:TYR225 4.4 14.5 1.0 CB H:LYS224 4.5 17.4 0.6 CB H:LYS224 4.5 16.9 0.4 O H:ASP221 4.5 21.8 1.0 C H:ASP222 4.6 22.7 1.0 OD1 H:ASP221 4.6 20.4 1.0 CA H:TYR225 4.7 13.5 1.0 HB2 H:ARG221A 4.8 26.7 1.0 C H:GLY223 4.9 18.1 1.0 HB3 H:LYS224 4.9 20.9 0.6 O H:HOH541 4.9 20.3 1.0 H H:ASP221 4.9 22.4 1.0 HB2 H:ASP189 4.9 19.0 1.0 HA H:ARG221A 5.0 25.2 1.0 HA3 H:GLY184 5.0 14.6 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)


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-2-Chlorothiophen Derivative (16E) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:13.9 occ:1.00 O H:THR172 2.3 14.2 1.0 O H:LYS169 2.4 14.3 0.4 O H:HOH525 2.4 31.5 1.0 O H:LYS169 2.4 14.2 0.6 O H:HOH605 2.4 16.7 1.0 O H:HOH502 2.8 22.5 1.0 HA H:ASP170 3.3 17.2 1.0 HG2 H:LYS169 3.4 25.2 0.6 C H:LYS169 3.5 14.3 0.4 C H:LYS169 3.5 14.1 0.6 H H:THR172 3.5 17.4 1.0 HG2 H:LYS169 3.5 22.8 0.4 C H:THR172 3.6 13.8 1.0 HA H:ARG173 3.6 17.6 1.0 HZ3 H:LYS169 3.8 29.4 0.4 CA H:ASP170 4.0 14.3 1.0 HG3 H:LYS169 4.1 25.2 0.6 N H:ASP170 4.2 14.0 1.0 CG H:LYS169 4.2 21.0 0.6 N H:THR172 4.3 14.5 1.0 HG3 H:LYS169 4.3 22.8 0.4 CG H:LYS169 4.3 19.0 0.4 HG23 H:THR172 4.4 19.1 1.0 C H:ASP170 4.4 14.7 1.0 CA H:ARG173 4.4 14.6 1.0 N H:ARG173 4.4 14.0 1.0 HA H:LYS169 4.5 17.4 0.4 HA H:LYS169 4.5 17.2 0.6 CA H:LYS169 4.6 14.3 0.6 O H:HOH424 4.6 38.3 1.0 CA H:THR172 4.6 14.2 1.0 CA H:LYS169 4.6 14.5 0.4 HG22 H:THR172 4.6 19.1 1.0 HE2 H:LYS169 4.6 30.9 0.6 NZ H:LYS169 4.7 24.5 0.4 O H:ASP170 4.7 14.4 1.0 OD1 H:ASP170 4.8 18.0 1.0 N H:SER171 4.8 13.3 1.0 HZ2 H:LYS169 4.9 29.4 0.4 CG2 H:THR172 4.9 15.9 1.0 HE3 H:LYS169 4.9 30.9 0.6 H H:SER171 4.9 16.0 1.0 CB H:LYS169 4.9 17.1 0.6 CB H:LYS169 5.0 16.5 0.4

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E) To Be Published.