Sodium in PDB 4dt7: Crystal Structure of Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C

All present enzymatic activity of Crystal Structure of Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C:
3.4.21.5; 3.4.21.69;

The structure of Crystal Structure of Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C, PDB code: 4dt7 was solved by N.Pozzi, S.Barranco-Medina, Z.Chen, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	35.70 / 1.90
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	46.395, 84.272, 66.363, 90.00, 94.59, 90.00
R / Rfree (%)	17.6 / 21.8

The binding sites of Sodium atom in the Crystal Structure of Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C (pdb code 4dt7). 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 Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C, PDB code: 4dt7:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C


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 Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:28.2 occ:1.00 O B:HOH564 2.2 29.7 1.0 O B:HOH544 2.3 35.8 1.0 O B:ARG221A 2.3 29.2 1.0 O B:LYS224 2.4 23.6 1.0 O B:HOH538 2.5 22.7 1.0 O B:HOH512 3.1 31.5 1.0 C B:ARG221A 3.4 31.3 1.0 C B:LYS224 3.5 23.6 1.0 O B:HOH523 3.7 27.5 1.0 N B:ARG221A 3.8 29.5 1.0 N B:LYS224 3.9 27.4 1.0 O B:HOH598 3.9 38.7 1.0 C B:ASP221 4.1 29.8 1.0 O B:TYR184A 4.1 27.2 1.0 CA B:LYS224 4.2 25.6 1.0 O B:HOH515 4.2 20.9 1.0 CA B:ARG221A 4.2 31.1 1.0 N B:ASP222 4.3 32.5 1.0 CA B:ASP221 4.4 28.3 1.0 N B:GLY223 4.5 31.4 1.0 CA B:ASP222 4.5 33.2 1.0 CB B:LYS224 4.5 25.5 1.0 O B:HOH631 4.5 41.1 1.0 N B:TYR225 4.5 22.1 1.0 OD1 B:ASP221 4.6 29.2 1.0 O B:ASP221 4.7 31.1 1.0 C B:ASP222 4.7 32.5 1.0 CA B:TYR225 4.8 20.8 1.0 C B:GLY223 5.0 29.3 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C


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 Thrombin Bound to the Activation Domain Qedqvdprlidgkmtrrgds of Protein C within 5.0Å range: probe atom residue distance (Å) B Occ D:Na302 b:24.4 occ:1.00 O D:ARG221A 2.3 23.4 1.0 O D:HOH446 2.3 23.2 1.0 O D:HOH461 2.3 28.3 1.0 O D:LYS224 2.4 19.7 1.0 O D:HOH415 2.6 19.5 1.0 O D:HOH424 2.8 23.6 1.0 C D:ARG221A 3.4 24.7 1.0 C D:LYS224 3.5 19.8 1.0 N D:ARG221A 3.8 23.1 1.0 O D:HOH468 3.8 20.8 1.0 N D:LYS224 3.9 22.5 1.0 C D:ASP221 4.0 23.5 1.0 O D:HOH441 4.1 30.0 1.0 O D:TYR184A 4.1 20.8 1.0 CA D:ARG221A 4.2 24.9 1.0 O D:HOH439 4.2 17.8 1.0 CA D:LYS224 4.2 21.3 1.0 N D:ASP222 4.3 26.1 1.0 N D:GLY223 4.3 25.2 1.0 CA D:ASP221 4.3 22.6 1.0 O D:HOH501 4.4 29.0 1.0 CA D:ASP222 4.4 26.9 1.0 O D:ASP221 4.4 23.9 1.0 CB D:LYS224 4.5 21.6 1.0 N D:TYR225 4.6 19.0 1.0 C D:ASP222 4.6 26.5 1.0 OD1 D:ASP221 4.7 24.3 1.0 CA D:TYR225 4.8 17.9 1.0 C D:GLY223 4.9 23.8 1.0

N.Pozzi, S.Barranco-Medina, Z.Chen, E.Di Cera. Exposure of R169 Controls Protein C Activation and Autoactivation. Blood V. 120 664 2012.
ISSN: ISSN 0006-4971
PubMed: 22535660
DOI: 10.1182/BLOOD-2012-03-415323