Sodium in PDB 6t3q: Thrombin in Complex with A D-Phe-Pro-2-Aminopyridine Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-2-Aminopyridine Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Phe-Pro-2-Aminopyridine Derivative, PDB code: 6t3q was solved by K.Ngo, C.Collins, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	18.51 / 1.33
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.009, 71.290, 72.572, 90.00, 100.59, 90.00
R / Rfree (%)	12.5 / 14.6

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-2-Aminopyridine Derivative (pdb code 6t3q). 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-2-Aminopyridine Derivative, PDB code: 6t3q:
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-2-Aminopyridine 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-2-Aminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na304 b:16.3 occ:1.00 O H:ARG221A 2.3 16.9 1.0 O H:HOH563 2.3 17.7 1.0 O H:HOH469 2.4 15.6 1.0 O H:LYS224 2.4 13.4 1.0 O H:HOH474 2.5 13.7 1.0 O H:HOH502 2.7 20.3 1.0 H H:LYS224 3.3 20.2 1.0 C H:ARG221A 3.3 17.3 1.0 C H:LYS224 3.4 13.1 1.0 HA H:ASP221 3.6 19.0 1.0 HA H:ASP222 3.8 24.0 1.0 HB2 H:LYS224 3.8 20.0 1.0 O H:HOH532 3.8 14.9 1.0 N H:ARG221A 3.8 17.1 1.0 H H:ARG221A 3.9 20.5 1.0 N H:LYS224 3.9 16.9 1.0 H H:GLY223 4.0 23.4 1.0 HA H:TYR225 4.0 13.8 1.0 O H:HOH464 4.0 21.4 1.0 C H:ASP221 4.0 16.7 1.0 O H:TYR184A 4.1 15.2 1.0 CA H:LYS224 4.2 15.1 1.0 CA H:ARG221A 4.2 17.6 1.0 N H:ASP222 4.2 19.9 1.0 O H:HOH494 4.3 14.2 1.0 N H:GLY223 4.3 19.5 1.0 CA H:ASP221 4.3 15.9 1.0 CA H:ASP222 4.3 20.0 1.0 N H:TYR225 4.4 12.5 1.0 CB H:LYS224 4.5 16.6 1.0 O H:ASP221 4.5 19.0 1.0 C H:ASP222 4.6 19.5 1.0 OD1 H:ASP221 4.6 16.4 1.0 CA H:TYR225 4.7 11.5 1.0 HB2 H:ARG221A 4.7 23.8 1.0 H H:ASP221 4.9 19.1 1.0 C H:GLY223 4.9 16.9 1.0 HA H:ARG221A 4.9 21.2 1.0 O H:HOH512 4.9 20.1 1.0 H H:ASP222 5.0 23.9 1.0 HA3 H:GLY184 5.0 14.0 1.0 HB3 H:LYS224 5.0 20.0 1.0 HB2 H:ASP189 5.0 14.0 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-2-Aminopyridine 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-2-Aminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:13.4 occ:1.00 O H:THR172 2.3 13.2 1.0 O H:LYS169 2.4 12.8 1.0 O H:HOH592 2.4 17.2 1.0 O H:HOH583 2.4 25.6 1.0 O H:HOH472 3.0 23.1 1.0 HA H:ASP170 3.2 15.7 1.0 HG2 H:LYS169 3.4 22.8 1.0 C H:LYS169 3.5 12.2 1.0 H H:THR172 3.5 14.9 1.0 C H:THR172 3.6 12.4 1.0 HA H:ARG173 3.6 15.6 1.0 CA H:ASP170 4.0 13.1 1.0 N H:ASP170 4.1 12.8 1.0 N H:THR172 4.3 12.5 1.0 CG H:LYS169 4.3 19.0 1.0 C H:ASP170 4.3 12.6 1.0 HG3 H:LYS169 4.4 22.8 1.0 O H:HOH457 4.4 36.5 1.0 CA H:ARG173 4.4 13.0 1.0 N H:ARG173 4.4 12.1 1.0 HG23 H:THR172 4.4 16.9 1.0 HA H:LYS169 4.5 14.4 1.0 HE2 H:LYS169 4.5 31.6 1.0 CA H:LYS169 4.6 12.0 1.0 CA H:THR172 4.6 12.8 1.0 HG22 H:THR172 4.7 16.9 1.0 OD1 H:ASP170 4.7 17.8 1.0 O H:ASP170 4.7 13.4 1.0 N H:SER171 4.8 12.0 1.0 H H:SER171 4.9 14.4 1.0 CB H:LYS169 5.0 14.1 1.0 CG2 H:THR172 5.0 14.1 1.0 H H:ASP170 5.0 15.3 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