Sodium in PDB 6fjt: 4-Chloro-Benzamidine in Complex with Thrombin

All present enzymatic activity of 4-Chloro-Benzamidine in Complex with Thrombin:
3.4.21.5;

The structure of 4-Chloro-Benzamidine in Complex with Thrombin, PDB code: 6fjt was solved by N.Abazi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.47 / 1.27
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.200, 71.319, 72.435, 90.00, 100.31, 90.00
R / Rfree (%)	13.3 / 15.1

The structure of 4-Chloro-Benzamidine in Complex with Thrombin also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the 4-Chloro-Benzamidine in Complex with Thrombin (pdb code 6fjt). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the 4-Chloro-Benzamidine in Complex with Thrombin, PDB code: 6fjt:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the 4-Chloro-Benzamidine in Complex with Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of 4-Chloro-Benzamidine in Complex with Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:14.6 occ:1.00 O H:LYS169 2.3 15.6 0.6 O H:THR172 2.3 15.4 1.0 O H:HOH558 2.4 24.1 1.0 O H:LYS169 2.4 15.5 0.4 O H:HOH470 2.6 22.4 1.0 HA H:ASP170 3.3 17.2 1.0 C H:LYS169 3.4 14.2 0.6 C H:LYS169 3.5 14.5 0.4 H H:THR172 3.5 17.5 1.0 C H:THR172 3.6 14.4 1.0 HA H:ARG173 3.7 18.3 1.0 CA H:ASP170 4.0 14.3 1.0 CG H:LYS169 4.1 17.4 0.4 N H:ASP170 4.2 14.3 1.0 HB3 H:LYS169 4.2 19.9 0.6 HG23 H:THR172 4.2 19.4 1.0 N H:THR172 4.3 14.6 1.0 C H:ASP170 4.4 14.8 1.0 CA H:ARG173 4.4 15.3 1.0 N H:ARG173 4.4 15.7 1.0 HA H:LYS169 4.5 17.1 0.6 HA H:LYS169 4.5 17.4 0.4 CA H:LYS169 4.5 14.2 0.6 CA H:LYS169 4.5 14.5 0.4 CA H:THR172 4.5 14.8 1.0 HG22 H:THR172 4.6 19.4 1.0 OD1 H:ASP170 4.7 18.6 1.0 O H:ASP170 4.8 15.6 1.0 N H:SER171 4.9 14.2 1.0 CB H:LYS169 4.9 16.6 0.6 CG2 H:THR172 4.9 16.1 1.0 CB H:LYS169 4.9 15.7 0.4 H H:SER171 4.9 17.0 1.0 C H:ARG173 4.9 15.9 1.0 O H:ILE174 5.0 15.8 1.0 H H:ASP170 5.0 17.2 0.4 H H:ASP170 5.0 17.2 0.6

Sodium binding site 2 out of 2 in the 4-Chloro-Benzamidine in Complex with Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of 4-Chloro-Benzamidine in Complex with Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:18.4 occ:1.00 O H:ARG221A 2.3 20.1 1.0 O H:LYS224 2.3 15.1 0.3 O H:HOH484 2.3 19.2 1.0 O H:HOH562 2.3 19.5 1.0 O H:LYS224 2.4 16.8 0.7 O H:HOH486 2.5 16.5 1.0 O H:HOH495 2.7 20.9 1.0 H H:LYS224 3.2 21.1 0.3 H H:LYS224 3.3 22.3 0.7 C H:ARG221A 3.4 20.9 1.0 C H:LYS224 3.4 15.3 0.3 C H:LYS224 3.5 15.9 0.7 HA H:ASP221 3.7 24.0 1.0 HA H:ASP222 3.7 26.9 1.0 N H:LYS224 3.8 17.6 0.3 HB2 H:LYS224 3.9 22.9 0.7 N H:LYS224 3.9 18.6 0.7 N H:ARG221A 3.9 20.5 1.0 H H:GLY223 3.9 24.8 1.0 O H:HOH516 3.9 17.1 1.0 H H:ARG221A 3.9 24.6 1.0 HB2 H:LYS224 3.9 18.5 0.3 O H:HOH513 4.0 23.5 1.0 HA H:TYR225 4.1 17.1 1.0 C H:ASP221 4.1 21.0 1.0 O H:TYR184A 4.1 18.0 1.0 CA H:LYS224 4.2 15.7 0.3 CA H:LYS224 4.2 16.8 0.7 N H:ASP222 4.2 22.1 1.0 O H:HOH494 4.2 17.6 1.0 CA H:ARG221A 4.2 21.4 1.0 N H:GLY223 4.2 20.7 1.0 CA H:ASP222 4.3 22.4 1.0 CA H:ASP221 4.4 20.0 1.0 N H:TYR225 4.5 14.9 1.0 CB H:LYS224 4.5 19.1 0.7 C H:ASP222 4.5 21.3 1.0 O H:ASP221 4.5 22.8 1.0 CB H:LYS224 4.6 15.4 0.3 OD1 H:ASP221 4.6 21.0 1.0 CA H:TYR225 4.7 14.3 1.0 HB2 H:ARG221A 4.8 26.7 1.0 C H:GLY223 4.8 18.8 1.0 H H:ASP221 4.9 22.3 1.0 HA H:ARG221A 4.9 25.6 1.0 O H:HOH499 5.0 21.2 1.0 H H:ASP222 5.0 26.5 1.0 HA3 H:GLY184 5.0 15.6 1.0 HB3 H:LYS224 5.0 22.9 0.7

A.Abazi, A.Heine, G.Klebe. 4-Chloro-Benzamidine in Complex with Thrombin To Be Published.