Sodium in PDB 6t4a: Thrombin in Complex with A D-Phe-Pro-P-Aminopyridine Derivative

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

The structure of Thrombin in Complex with A D-Phe-Pro-P-Aminopyridine Derivative, PDB code: 6t4a 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)	35.63 / 1.31
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.149, 71.260, 72.496, 90.00, 100.59, 90.00
R / Rfree (%)	12.7 / 14.8

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-P-Aminopyridine Derivative (pdb code 6t4a). 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-P-Aminopyridine Derivative, PDB code: 6t4a:
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-P-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-P-Aminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na305 b:13.8 occ:1.00 O H:ARG221A 2.3 14.8 1.0 O H:HOH584 2.4 12.9 1.0 O H:HOH461 2.4 14.4 1.0 O H:LYS224 2.4 12.1 1.0 O H:HOH483 2.5 11.8 1.0 O H:HOH498 2.7 16.2 1.0 H H:LYS224 3.3 17.6 1.0 C H:ARG221A 3.4 16.1 1.0 C H:LYS224 3.4 11.8 1.0 HA H:ASP221 3.6 17.4 1.0 HA H:ASP222 3.8 21.3 1.0 HB2 H:LYS224 3.8 16.9 1.0 N H:LYS224 3.9 14.6 1.0 N H:ARG221A 3.9 14.8 1.0 O H:HOH519 3.9 12.0 1.0 H H:GLY223 3.9 21.1 1.0 H H:ARG221A 3.9 17.8 1.0 O H:HOH475 4.0 18.7 1.0 C H:ASP221 4.0 14.1 1.0 HA H:TYR225 4.0 11.9 1.0 O H:TYR184A 4.1 13.8 1.0 CA H:LYS224 4.1 13.8 1.0 N H:ASP222 4.2 17.4 1.0 CA H:ARG221A 4.2 16.4 1.0 O H:HOH496 4.3 11.9 1.0 N H:GLY223 4.3 17.6 1.0 CA H:ASP221 4.3 14.5 1.0 CA H:ASP222 4.3 17.8 1.0 O H:ASP221 4.4 16.4 1.0 N H:TYR225 4.4 10.9 1.0 CB H:LYS224 4.5 14.1 1.0 C H:ASP222 4.5 17.5 1.0 OD1 H:ASP221 4.6 14.3 1.0 CA H:TYR225 4.7 9.9 1.0 C H:GLY223 4.9 14.5 1.0 HB2 H:ARG221A 4.9 19.1 1.0 O H:HOH418 4.9 14.2 1.0 HA H:ARG221A 4.9 19.7 1.0 HB2 H:ASP189 5.0 12.3 1.0 H H:ASP221 5.0 16.4 1.0 HB3 H:LYS224 5.0 16.9 1.0 H H:ASP222 5.0 20.9 1.0 HA3 H:GLY184 5.0 12.7 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-P-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-P-Aminopyridine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na306 b:11.7 occ:1.00 O H:HOH468 2.4 14.6 1.0 O H:PHE204A 2.4 9.8 1.0 C H:PHE204A 3.5 9.5 1.0 HA H:PHE204A 3.5 12.1 1.0 CA H:PHE204A 4.1 10.0 1.0 HA H:ASN204B 4.2 14.3 1.0 O H:PRO204 4.4 10.4 1.0 N H:ASN204B 4.6 10.5 1.0 HB3 H:PHE204A 4.7 13.9 1.0 CA H:ASN204B 4.9 11.9 1.0 CB H:PHE204A 5.0 11.6 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