Sodium in PDB 4hfp: Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban

All present enzymatic activity of Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban:
3.4.21.5;

The structure of Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban, PDB code: 4hfp was solved by N.Pozzi, Z.Chen, F.Zapata, W.Lin, S.Barranco-Medina, L.A.Pelc, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	40.42 / 2.40
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	77.229, 77.229, 94.875, 90.00, 90.00, 90.00
R / Rfree (%)	16.7 / 23.8

The binding sites of Sodium atom in the Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban (pdb code 4hfp). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban, PDB code: 4hfp:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:26.4 occ:1.00 O B:HOH529 2.4 14.4 1.0 O B:HOH516 2.5 17.4 1.0 O B:LYS224 2.6 29.6 1.0 O B:ARG221A 2.9 34.5 1.0 O B:HOH509 3.0 18.4 1.0 O B:HOH517 3.1 28.0 1.0 O B:TYR184A 3.6 30.9 1.0 O B:HOH515 3.7 32.6 1.0 C B:LYS224 3.8 30.1 1.0 C B:ARG221A 3.8 36.8 1.0 C B:ASP221 4.1 35.2 1.0 N B:ARG221A 4.2 35.6 1.0 N B:LYS224 4.3 33.8 1.0 O B:ASP221 4.3 36.6 1.0 CA B:ASP221 4.4 33.5 1.0 OD1 B:ASP221 4.4 31.9 1.0 CA B:LYS224 4.6 32.4 1.0 N B:GLY223 4.6 36.4 1.0 N B:ASP222 4.6 39.0 1.0 CA B:ASP222 4.7 39.0 1.0 CA B:ARG221A 4.7 37.6 1.0 C B:TYR184A 4.8 31.3 1.0 N B:TYR225 4.8 28.9 1.0 CD2 B:TYR225 4.9 27.1 1.0 CA B:TYR225 4.9 27.2 1.0 N B:TYR184A 5.0 29.5 1.0 CB B:LYS224 5.0 33.5 1.0

Sodium binding site 2 out of 2 in the Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Thrombin Mutant S195A Bound to the Active Site Inhibitor Argatroban within 5.0Å range: probe atom residue distance (Å) B Occ D:Na401 b:27.5 occ:1.00 O D:LYS224 2.4 40.3 1.0 O D:ARG221A 2.6 45.1 1.0 O D:HOH510 3.3 23.1 1.0 N D:ARG221A 3.5 46.6 1.0 C D:LYS224 3.6 39.8 1.0 C D:ARG221A 3.7 47.0 1.0 C D:ASP221 4.0 47.6 1.0 CA D:ASP221 4.0 46.1 1.0 CA D:ARG221A 4.2 48.0 1.0 OD1 D:ASP221 4.3 46.9 1.0 N D:LYS224 4.4 42.1 1.0 O D:TYR184A 4.5 45.9 1.0 CA D:LYS224 4.5 41.1 1.0 N D:TYR225 4.6 38.4 1.0 CA D:TYR225 4.6 37.2 1.0 O D:HOH511 4.6 28.9 1.0 N D:ASP222 4.7 48.7 1.0 N D:ASP221 4.7 45.6 1.0 O D:GLY188 4.7 40.8 1.0 CB D:LYS224 4.8 42.4 1.0 O D:ASP221 4.8 49.8 1.0

N.Pozzi, Z.Chen, F.Zapata, W.Niu, S.Barranco-Medina, L.A.Pelc, E.Di Cera. Autoactivation of Thrombin Precursors. J.Biol.Chem. V. 288 11601 2013.
ISSN: ISSN 0021-9258
PubMed: 23467412
DOI: 10.1074/JBC.M113.451542