Sodium in PDB 6t57: Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative, PDB code: 6t57 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)	43.73 / 1.57
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.290, 71.660, 73.245, 90.00, 100.68, 90.00
R / Rfree (%)	19.3 / 21.3

The structure of Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative also contains other interesting chemical elements:

Fluorine

(F)

3 atoms

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative (pdb code 6t57). 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 A D-Phe-Pro-N-Amidinopiperidine Derivative, PDB code: 6t57:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative


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 A D-Phe-Pro-N-Amidinopiperidine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:0.9 occ:1.00 O H:HOH449 2.4 43.0 1.0 O H:HOH492 2.4 32.0 1.0 O H:HOH467 2.4 27.2 1.0 O H:ARG221A 2.4 29.1 1.0 O H:LYS224 2.5 27.7 1.0 O H:HOH503 2.7 39.8 1.0 C H:ARG221A 3.5 35.4 1.0 C H:LYS224 3.6 24.5 1.0 N H:LYS224 3.6 28.7 1.0 O H:TYR184A 3.7 31.9 1.0 O H:HOH524 3.7 39.1 1.0 N H:GLY223 3.8 36.0 1.0 CA H:ASP222 4.0 39.8 1.0 CA H:LYS224 4.2 26.2 1.0 C H:ASP222 4.2 34.2 1.0 N H:ASP222 4.2 31.6 1.0 O H:HOH446 4.4 28.5 1.0 C H:GLY223 4.5 35.2 1.0 N H:ARG221A 4.5 28.8 1.0 CA H:GLY223 4.6 34.7 1.0 O H:HOH485 4.6 30.9 1.0 C H:ASP221 4.6 30.7 1.0 CA H:ARG221A 4.6 29.4 1.0 N H:TYR225 4.7 25.5 1.0 CB H:LYS224 4.7 25.4 1.0 O H:ASP221 4.8 33.1 1.0 O H:HOH418 4.8 28.8 1.0 C H:TYR184A 4.9 34.0 1.0 CD2 H:TYR225 4.9 25.7 1.0 CE2 H:TYR225 5.0 27.6 1.0 CA H:TYR225 5.0 22.1 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative


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 A D-Phe-Pro-N-Amidinopiperidine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na304 b:23.1 occ:0.49 O H:HOH442 2.4 44.5 1.0 O H:LYS169 2.5 27.9 1.0 O H:THR172 2.6 30.1 1.0 C H:LYS169 3.5 29.3 1.0 O H:HOH409 3.5 30.4 1.0 C H:THR172 3.8 31.5 1.0 CA H:ASP170 3.8 26.6 1.0 N H:ASP170 4.1 25.2 1.0 C H:ASP170 4.3 23.7 1.0 CG H:LYS169 4.3 38.4 1.0 N H:THR172 4.4 24.1 1.0 OD1 H:ASP170 4.5 31.4 1.0 O H:ASP170 4.6 27.1 1.0 CA H:LYS169 4.6 26.2 1.0 CA H:ARG173 4.6 26.2 1.0 N H:ARG173 4.6 25.8 1.0 NZ H:LYS169 4.7 52.1 1.0 CA H:THR172 4.7 25.8 1.0 N H:SER171 4.8 23.7 1.0 CB H:LYS169 5.0 27.4 1.0

K.Ngo, N.Abazi, A.Heine, G.Klebe. Thrombin in Complex with A D-Phe-Pro-N-Amidinopiperidine Derivative To Be Published.