Sodium in PDB 6tdt: Thrombin in Complex with A D-Diphe-Pro-P-Pyridine Derivative

All present enzymatic activity of Thrombin in Complex with A D-Diphe-Pro-P-Pyridine Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Diphe-Pro-P-Pyridine Derivative, PDB code: 6tdt was solved by K.Ngo, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.36 / 1.53
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	69.872, 71.726, 72.099, 90.00, 100.18, 90.00
R / Rfree (%)	16 / 17.7

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

Sodium binding site 1 out of 2 in the Thrombin in Complex with A D-Diphe-Pro-P-Pyridine 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-Diphe-Pro-P-Pyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:13.6 occ:1.00 O H:THR172 2.4 15.3 1.0 O H:LYS169 2.4 15.8 1.0 O H:HOH576 2.5 24.6 1.0 O H:HOH468 2.6 26.1 1.0 HG2 H:LYS169 3.4 28.8 1.0 HA H:ASP170 3.5 20.4 1.0 C H:LYS169 3.5 16.9 1.0 H H:THR172 3.6 16.4 1.0 C H:THR172 3.6 15.1 1.0 HA H:ARG173 3.7 18.9 1.0 HG3 H:LYS169 4.0 28.8 1.0 CG H:LYS169 4.1 23.9 1.0 CA H:ASP170 4.2 17.0 1.0 HG23 H:THR172 4.2 21.8 1.0 HE2 H:LYS169 4.2 42.5 1.0 N H:ASP170 4.3 15.6 1.0 HG22 H:THR172 4.3 21.8 1.0 O H:HOH526 4.3 32.3 1.0 N H:THR172 4.3 13.7 1.0 HA H:LYS169 4.4 18.7 1.0 CA H:ARG173 4.5 15.8 1.0 N H:ARG173 4.5 13.6 1.0 CA H:LYS169 4.5 15.6 1.0 C H:ASP170 4.5 16.1 1.0 CA H:THR172 4.6 13.5 1.0 CG2 H:THR172 4.7 18.1 1.0 OD1 H:ASP170 4.9 21.0 1.0 CB H:LYS169 4.9 17.8 1.0 O H:ASP170 5.0 15.7 1.0 N H:SER171 5.0 14.2 1.0 H H:SER171 5.0 17.1 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Diphe-Pro-P-Pyridine 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-Diphe-Pro-P-Pyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na303 b:15.9 occ:1.00 O H:HOH580 2.2 18.5 1.0 O H:ARG221A 2.3 17.5 1.0 O H:LYS224 2.4 15.6 1.0 O H:HOH459 2.4 17.4 1.0 O H:HOH462 2.4 15.4 1.0 O H:HOH471 2.9 20.3 1.0 H H:LYS224 3.2 19.0 1.0 C H:ARG221A 3.3 20.4 1.0 C H:LYS224 3.4 13.6 1.0 HA H:ASP221 3.7 20.9 1.0 HA H:ASP222 3.7 24.6 1.0 HB2 H:LYS224 3.8 21.3 1.0 O H:HOH516 3.8 16.2 1.0 N H:LYS224 3.8 15.8 1.0 N H:ARG221A 3.9 18.1 1.0 H H:GLY223 3.9 24.0 1.0 H H:ARG221A 3.9 21.7 1.0 HA H:TYR225 4.0 16.4 1.0 O H:HOH465 4.0 20.9 1.0 C H:ASP221 4.1 18.7 1.0 CA H:LYS224 4.1 17.3 1.0 O H:TYR184A 4.1 17.9 1.0 N H:ASP222 4.2 19.9 1.0 CA H:ARG221A 4.2 16.8 1.0 N H:GLY223 4.3 20.0 1.0 O H:HOH514 4.3 14.8 1.0 CA H:ASP222 4.3 20.5 1.0 CA H:ASP221 4.3 17.4 1.0 N H:TYR225 4.4 15.3 1.0 CB H:LYS224 4.5 17.7 1.0 C H:ASP222 4.5 19.7 1.0 O H:ASP221 4.5 20.5 1.0 OD1 H:ASP221 4.6 17.3 1.0 CA H:TYR225 4.7 13.7 1.0 HB2 H:ARG221A 4.7 22.6 1.0 O H:HOH513 4.8 20.3 1.0 C H:GLY223 4.8 20.7 1.0 H H:ASP221 4.9 18.9 1.0 HA H:ARG221A 4.9 20.1 1.0 HB2 H:ASP189 4.9 16.8 1.0 HA3 H:GLY184 5.0 18.0 1.0 H H:ASP222 5.0 23.9 1.0

K.Ngo, C.Collins-Kautz, S.Gerstenecker, B.Wagner, A.Heine, G.Klebe. Protein-Induced Change in Ligand Protonation During Trypsin and Thrombin Binding: Hint on Differences in Selectivity Determinants of Both Proteins? J.Med.Chem. V. 63 3274 2020.
ISSN: ISSN 0022-2623
PubMed: 32011145
DOI: 10.1021/ACS.JMEDCHEM.9B02061