Sodium in PDB 6yb6: Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C):
3.4.21.5;

The structure of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C), PDB code: 6yb6 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)	35.59 / 1.33
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.436, 71.2, 72.316, 90, 100.2, 90
R / Rfree (%)	13.1 / 15.3

The structure of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) (pdb code 6yb6). 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-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C), PDB code: 6yb6:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C)


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-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:16.2 occ:1.00 O H:LYS169 2.3 13.9 0.3 O H:THR172 2.4 15.6 1.0 O H:LYS169 2.4 14.4 0.7 O H:HOH527 2.4 27.8 1.0 O H:HOH469 3.0 25.9 1.0 HA H:ASP170 3.3 16.4 1.0 HG2 H:LYS169 3.4 20.8 0.3 C H:LYS169 3.5 13.6 0.3 C H:LYS169 3.5 13.8 0.7 HG2 H:LYS169 3.5 24.3 0.7 H H:THR172 3.5 16.4 1.0 C H:THR172 3.6 14.3 1.0 HA H:ARG173 3.7 17.9 1.0 HZ3 H:LYS169 3.7 32.4 0.7 CA H:ASP170 4.0 13.7 1.0 N H:ASP170 4.1 13.4 1.0 CG H:LYS169 4.3 17.3 0.3 N H:THR172 4.3 13.7 1.0 CG H:LYS169 4.3 20.2 0.7 HG3 H:LYS169 4.3 24.3 0.7 HG3 H:LYS169 4.3 20.8 0.3 C H:ASP170 4.4 14.0 1.0 N H:ARG173 4.4 14.4 1.0 CA H:ARG173 4.4 14.9 1.0 HA H:LYS169 4.5 16.2 0.7 HA H:LYS169 4.5 16.2 0.3 HG23 H:THR172 4.5 18.0 1.0 CA H:LYS169 4.5 13.5 0.7 CA H:LYS169 4.5 13.5 0.3 NZ H:LYS169 4.5 27.0 0.7 CA H:THR172 4.6 14.0 1.0 HE2 H:LYS169 4.6 24.6 0.3 OD1 H:ASP170 4.7 18.7 1.0 HZ2 H:LYS169 4.7 32.4 0.7 HG22 H:THR172 4.7 18.0 1.0 O H:ASP170 4.8 14.7 1.0 N H:SER171 4.8 13.2 1.0 H H:SER171 4.9 15.8 1.0 CB H:LYS169 4.9 16.7 0.7 CB H:LYS169 4.9 15.4 0.3 HZ1 H:LYS169 4.9 32.4 0.7 H H:ASP170 5.0 16.0 0.7 H H:ASP170 5.0 16.0 0.3

Sodium binding site 2 out of 2 in the Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C)


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-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:16.7 occ:1.00 O H:ARG221A 2.3 18.3 1.0 O H:HOH560 2.3 17.5 1.0 O H:HOH481 2.4 17.9 1.0 O H:LYS224 2.4 15.4 0.6 O H:LYS224 2.4 15.5 0.4 O H:HOH489 2.4 14.4 1.0 O H:HOH499 2.7 19.1 1.0 H H:LYS224 3.2 19.0 0.6 H H:LYS224 3.3 19.4 0.4 C H:ARG221A 3.4 18.7 1.0 C H:LYS224 3.4 14.9 0.4 C H:LYS224 3.4 14.6 0.6 HA H:ASP221 3.7 22.3 1.0 HA H:ASP222 3.7 24.8 1.0 HB2 H:LYS224 3.8 17.8 0.6 HB2 H:LYS224 3.8 19.3 0.4 N H:ARG221A 3.9 19.1 1.0 N H:LYS224 3.9 15.8 0.6 N H:LYS224 3.9 16.2 0.4 H H:ARG221A 3.9 23.0 1.0 O H:HOH511 3.9 15.6 1.0 H H:GLY223 4.0 22.0 1.0 O H:HOH491 4.0 21.8 1.0 HA H:TYR225 4.1 16.0 1.0 C H:ASP221 4.1 19.1 1.0 O H:TYR184A 4.1 16.1 1.0 CA H:LYS224 4.1 15.7 0.4 CA H:LYS224 4.2 15.0 0.6 N H:ASP222 4.2 20.4 1.0 O H:HOH502 4.2 15.8 1.0 CA H:ARG221A 4.2 20.1 1.0 N H:GLY223 4.3 18.4 1.0 CA H:ASP222 4.3 20.6 1.0 CA H:ASP221 4.4 18.6 1.0 N H:TYR225 4.5 13.8 1.0 CB H:LYS224 4.5 16.1 0.4 CB H:LYS224 4.5 14.8 0.6 C H:ASP222 4.5 19.6 1.0 O H:ASP221 4.5 21.1 1.0 OD1 H:ASP221 4.6 18.5 1.0 CA H:TYR225 4.7 13.3 1.0 O H:HOH555 4.8 31.4 1.0 HB2 H:ARG221A 4.8 26.9 1.0 C H:GLY223 4.9 16.2 1.0 HB3 H:LYS224 4.9 19.3 0.4 HA H:ARG221A 4.9 24.1 1.0 H H:ASP221 5.0 21.8 1.0 HA3 H:GLY184 5.0 15.1 1.0 H H:ASP222 5.0 24.5 1.0

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) To Be Published.