Sodium in PDB 3lu9: Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1

All present enzymatic activity of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1:
3.4.21.5;

The structure of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1, PDB code: 3lu9 was solved by P.S.Gandhi, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	28.07 / 1.80
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	46.334, 50.171, 85.502, 76.39, 83.93, 73.74
R / Rfree (%)	19.3 / 23.6

The binding sites of Sodium atom in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1 (pdb code 3lu9). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1, PDB code: 3lu9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1 within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:26.2 occ:1.00 O B:HOH520 2.3 11.7 1.0 O B:ARG221A 2.3 15.0 1.0 O B:LYS224 2.4 14.3 1.0 O B:HOH2 2.4 7.8 1.0 O B:HOH515 2.5 6.5 1.0 O B:HOH278 2.7 9.3 1.0 C B:ARG221A 3.4 16.2 1.0 C B:LYS224 3.5 14.4 1.0 N B:LYS224 3.8 15.8 1.0 N B:ARG221A 3.9 14.3 1.0 C B:ASP221 4.0 15.2 1.0 O B:HOH258 4.0 9.0 1.0 O B:HOH512 4.0 9.0 1.0 N B:GLY223 4.1 19.3 1.0 O B:TYR184A 4.2 15.2 1.0 CA B:LYS224 4.2 14.6 1.0 N B:ASP222 4.2 17.4 1.0 CA B:ARG221A 4.3 15.3 1.0 O B:HOH296 4.3 4.9 1.0 CA B:ASP222 4.3 19.2 1.0 CA B:ASP221 4.3 14.8 1.0 O B:HOH330 4.4 13.8 1.0 C B:ASP222 4.5 19.8 1.0 O B:ASP221 4.5 16.6 1.0 N B:TYR225 4.5 13.4 1.0 CB B:LYS224 4.6 15.0 1.0 OD1 B:ASP221 4.6 18.4 1.0 C B:GLY223 4.8 17.1 1.0 CA B:TYR225 4.8 12.2 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Human Thrombin Mutant S195A in Complex with the Extracellular Fragment of Human PAR1 within 5.0Å range: probe atom residue distance (Å) B Occ E:Na401 b:27.6 occ:1.00 O E:ARG221A 2.3 18.5 1.0 O E:LYS224 2.4 19.3 1.0 O E:HOH513 2.4 11.2 1.0 O E:HOH508 2.5 17.0 1.0 O E:HOH510 2.5 9.6 1.0 O E:HOH597 2.6 15.4 1.0 C E:ARG221A 3.4 19.1 1.0 C E:LYS224 3.4 20.9 1.0 N E:LYS224 3.8 23.1 1.0 N E:ARG221A 3.9 16.4 1.0 O E:HOH600 4.0 13.4 1.0 O E:HOH509 4.0 6.5 1.0 O E:TYR184A 4.1 20.3 1.0 CA E:LYS224 4.1 22.6 1.0 C E:ASP221 4.1 17.0 1.0 N E:GLY223 4.1 24.4 1.0 O E:HOH253 4.2 9.2 1.0 N E:ASP222 4.2 20.4 1.0 CA E:ASP222 4.3 22.4 1.0 CA E:ARG221A 4.3 19.0 1.0 CA E:ASP221 4.4 15.1 1.0 C E:ASP222 4.5 23.8 1.0 N E:TYR225 4.5 21.0 1.0 CB E:LYS224 4.5 20.9 1.0 O E:HOH310 4.5 16.8 1.0 OD1 E:ASP221 4.6 17.5 1.0 O E:ASP221 4.6 17.1 1.0 C E:GLY223 4.8 25.4 1.0 CA E:TYR225 4.8 20.5 1.0 CA E:GLY223 5.0 26.6 1.0 CD1 E:TYR225 5.0 22.0 1.0

P.S.Gandhi, Z.Chen, E.Di Cera. Crystal Structure of Thrombin Bound to the Uncleaved Extracellular Fragment of PAR1. J.Biol.Chem. V. 285 15393 2010.
ISSN: ISSN 0021-9258
PubMed: 20236938
DOI: 10.1074/JBC.M110.115337