Sodium in PDB 6t56: Thrombin in Complex with Benzylamine

All present enzymatic activity of Thrombin in Complex with Benzylamine:
3.4.21.5;

The structure of Thrombin in Complex with Benzylamine, PDB code: 6t56 was solved by K.Ngo, 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)	34.69 / 1.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.553, 71.037, 72.806, 90.00, 100.48, 90.00
R / Rfree (%)	14 / 16.3

The binding sites of Sodium atom in the Thrombin in Complex with Benzylamine (pdb code 6t56). 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 Benzylamine, PDB code: 6t56:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with Benzylamine


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 Benzylamine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:18.3 occ:1.00 O H:HOH570 2.3 19.4 1.0 O H:ARG221A 2.3 18.7 1.0 O H:HOH477 2.4 19.4 1.0 O H:LYS224 2.4 15.9 1.0 O H:HOH479 2.5 16.1 1.0 O H:HOH517 2.7 22.0 1.0 H H:LYS224 3.3 20.8 1.0 C H:ARG221A 3.4 19.4 1.0 C H:LYS224 3.4 15.4 1.0 HA H:ASP221 3.7 22.2 1.0 HA H:ASP222 3.8 25.8 1.0 HB2 H:LYS224 3.8 22.2 1.0 N H:ARG221A 3.9 18.8 1.0 H H:GLY223 3.9 24.4 1.0 N H:LYS224 3.9 17.4 1.0 O H:HOH524 3.9 17.0 1.0 H H:ARG221A 3.9 22.6 1.0 O H:HOH491 4.0 22.9 1.0 HA H:TYR225 4.0 17.4 1.0 C H:ASP221 4.0 19.4 1.0 CA H:LYS224 4.1 17.1 1.0 O H:TYR184A 4.1 17.8 1.0 N H:ASP222 4.2 21.0 1.0 CA H:ARG221A 4.2 20.4 1.0 N H:GLY223 4.2 20.3 1.0 O H:HOH490 4.3 17.8 1.0 CA H:ASP222 4.3 21.5 1.0 CA H:ASP221 4.4 18.5 1.0 N H:TYR225 4.4 15.1 1.0 O H:ASP221 4.5 21.1 1.0 CB H:LYS224 4.5 18.5 1.0 C H:ASP222 4.5 20.8 1.0 OD1 H:ASP221 4.6 19.6 1.0 CA H:TYR225 4.7 14.5 1.0 HB2 H:ARG221A 4.8 26.0 1.0 C H:GLY223 4.8 19.1 1.0 O H:HOH488 4.9 21.1 1.0 HA H:ARG221A 4.9 24.5 1.0 H H:ASP221 5.0 22.3 1.0 H H:ASP222 5.0 25.2 1.0 HB2 H:ASP189 5.0 18.6 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with Benzylamine


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 Benzylamine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:15.9 occ:1.00 O H:THR172 2.3 14.9 1.0 O H:HOH573 2.3 19.0 1.0 O H:LYS169 2.4 16.4 1.0 O H:HOH533 2.4 22.7 1.0 O H:HOH482 2.6 23.5 1.0 HA H:ASP170 3.2 18.4 1.0 C H:LYS169 3.4 15.1 1.0 H H:THR172 3.5 18.1 1.0 C H:THR172 3.6 14.4 1.0 HA H:ARG173 3.7 18.2 1.0 CA H:ASP170 4.0 15.4 1.0 HB3 H:LYS169 4.1 20.1 1.0 N H:ASP170 4.1 14.9 1.0 N H:THR172 4.3 15.1 1.0 C H:ASP170 4.4 15.9 1.0 HG23 H:THR172 4.4 19.8 1.0 CA H:ARG173 4.4 15.2 1.0 N H:ARG173 4.4 14.6 1.0 HA H:LYS169 4.4 17.9 1.0 CA H:LYS169 4.5 14.9 1.0 HG22 H:THR172 4.5 19.8 1.0 O H:HOH466 4.5 41.7 1.0 CA H:THR172 4.5 15.3 1.0 OD1 H:ASP170 4.6 19.1 1.0 O H:ASP170 4.8 16.7 1.0 CB H:LYS169 4.8 16.7 1.0 N H:SER171 4.9 15.4 1.0 CG2 H:THR172 4.9 16.5 1.0 H H:SER171 4.9 18.5 1.0 C H:ARG173 4.9 15.5 1.0 H H:ASP170 5.0 17.9 1.0 O H:ILE174 5.0 15.7 1.0

K.Ngo, N.Abazi, A.Heine, G.Klebe. Thrombin in Complex with Benzylamine To Be Published.