Sodium in PDB 6t55: Thrombin in Complex with Methylbenzylamine

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

The structure of Thrombin in Complex with Methylbenzylamine, PDB code: 6t55 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)	49.66 / 1.39
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.271, 71.336, 72.395, 90.00, 100.18, 90.00
R / Rfree (%)	15.4 / 17.2

The binding sites of Sodium atom in the Thrombin in Complex with Methylbenzylamine (pdb code 6t55). 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 Methylbenzylamine, PDB code: 6t55:
Jump to Sodium binding site number: 1; 2;

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


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 Methylbenzylamine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:18.8 occ:1.00 O H:ARG221A 2.3 21.6 1.0 O H:HOH581 2.3 20.1 1.0 O H:HOH485 2.4 19.4 1.0 O H:LYS224 2.4 18.9 1.0 O H:HOH472 2.5 17.4 1.0 O H:HOH484 2.7 21.8 1.0 H H:LYS224 3.3 24.3 1.0 C H:ARG221A 3.4 23.3 1.0 C H:LYS224 3.4 18.5 1.0 HA H:ASP221 3.7 24.0 1.0 HA H:ASP222 3.8 30.2 1.0 HB2 H:LYS224 3.8 25.4 1.0 O H:HOH510 3.8 18.2 1.0 N H:LYS224 3.8 20.3 1.0 N H:ARG221A 3.9 20.9 1.0 H H:ARG221A 3.9 25.1 1.0 H H:GLY223 3.9 30.3 1.0 HA H:TYR225 4.0 20.8 1.0 O H:HOH482 4.0 25.1 1.0 C H:ASP221 4.1 21.5 1.0 CA H:LYS224 4.1 20.2 1.0 O H:TYR184A 4.1 21.9 1.0 CA H:ARG221A 4.2 23.1 1.0 N H:ASP222 4.2 25.6 1.0 O H:HOH465 4.3 18.9 1.0 N H:GLY223 4.3 25.3 1.0 CA H:ASP222 4.3 25.2 1.0 CA H:ASP221 4.4 20.0 1.0 N H:TYR225 4.4 17.5 1.0 CB H:LYS224 4.4 21.1 1.0 O H:ASP221 4.5 24.4 1.0 C H:ASP222 4.5 24.6 1.0 OD1 H:ASP221 4.6 21.7 1.0 CA H:TYR225 4.7 17.4 1.0 HB2 H:ARG221A 4.8 29.4 1.0 C H:GLY223 4.8 21.6 1.0 HA H:ARG221A 4.9 27.8 1.0 HB3 H:LYS224 4.9 25.4 1.0 H H:ASP221 4.9 23.5 1.0 O H:HOH478 5.0 19.5 1.0 HA3 H:GLY184 5.0 20.4 1.0

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


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 Methylbenzylamine within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:17.4 occ:1.00 O H:THR172 2.3 18.0 1.0 O H:LYS169 2.4 18.1 1.0 O H:HOH561 2.4 23.3 1.0 O H:HOH455 2.6 24.6 1.0 HA H:ASP170 3.3 22.0 1.0 C H:LYS169 3.4 17.6 1.0 H H:THR172 3.5 21.7 1.0 C H:THR172 3.6 17.9 1.0 HA H:ARG173 3.7 21.2 1.0 CA H:ASP170 4.0 18.4 1.0 N H:ASP170 4.1 17.6 1.0 HB3 H:LYS169 4.2 23.7 1.0 N H:THR172 4.3 18.1 1.0 HG23 H:THR172 4.3 22.4 1.0 C H:ASP170 4.4 18.7 1.0 HA H:LYS169 4.4 20.9 1.0 CA H:ARG173 4.4 17.7 1.0 N H:ARG173 4.4 16.9 1.0 O H:HOH476 4.5 41.3 1.0 HG22 H:THR172 4.5 22.4 1.0 CA H:LYS169 4.5 17.4 1.0 CA H:THR172 4.5 17.9 1.0 OD1 H:ASP170 4.7 22.7 1.0 O H:ASP170 4.8 19.0 1.0 CG2 H:THR172 4.8 18.7 1.0 CB H:LYS169 4.8 19.8 1.0 N H:SER171 4.9 18.4 1.0 O H:HOH603 4.9 45.5 1.0 H H:SER171 4.9 22.1 1.0 C H:ARG173 5.0 18.8 1.0 O H:ILE174 5.0 18.0 1.0 H H:ASP170 5.0 21.1 1.0

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