Sodium in PDB 3r3g: Structure of Human Thrombin with Residues 145-150 of Murine Thrombin.

All present enzymatic activity of Structure of Human Thrombin with Residues 145-150 of Murine Thrombin.:
3.4.21.5;

The structure of Structure of Human Thrombin with Residues 145-150 of Murine Thrombin., PDB code: 3r3g was solved by N.Pozzi, R.Chen, Z.Chen, A.Bah, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	30.13 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	116.072, 48.058, 53.722, 90.00, 92.08, 90.00
R / Rfree (%)	18.4 / 22.2

The binding sites of Sodium atom in the Structure of Human Thrombin with Residues 145-150 of Murine Thrombin. (pdb code 3r3g). 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 Human Thrombin with Residues 145-150 of Murine Thrombin., PDB code: 3r3g:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Structure of Human Thrombin with Residues 145-150 of Murine Thrombin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Structure of Human Thrombin with Residues 145-150 of Murine Thrombin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:28.0 occ:1.00 O B:HOH439 2.3 35.4 1.0 O B:HOH430 2.3 30.3 1.0 O B:HOH432 2.3 26.8 1.0 O B:LYS224 2.3 29.5 1.0 O B:ARG221A 2.4 32.7 1.0 O B:HOH309 2.7 32.3 1.0 C B:ARG221A 3.4 34.9 1.0 C B:LYS224 3.5 28.6 1.0 N B:ARG221A 3.8 34.1 1.0 N B:LYS224 3.9 31.3 1.0 O B:HOH11 3.9 23.6 1.0 O B:HOH365 4.0 37.0 1.0 C B:ASP221 4.0 34.4 1.0 O B:TYR184A 4.0 29.1 1.0 O B:HOH259 4.1 29.2 1.0 CA B:LYS224 4.2 30.2 1.0 CA B:ARG221A 4.2 35.3 1.0 N B:ASP222 4.3 36.0 1.0 CA B:ASP221 4.3 33.0 1.0 N B:GLY223 4.4 35.1 1.0 CA B:ASP222 4.4 36.6 1.0 N B:TYR225 4.5 27.0 1.0 O B:ASP221 4.6 35.0 1.0 CB B:LYS224 4.6 30.4 1.0 OD1 B:ASP221 4.6 31.4 1.0 C B:ASP222 4.7 36.5 1.0 CA B:TYR225 4.8 26.0 1.0 O B:HOH317 4.8 31.9 1.0 C B:GLY223 5.0 32.8 1.0 CD1 B:TYR225 5.0 27.1 1.0

Sodium binding site 2 out of 2 in the Structure of Human Thrombin with Residues 145-150 of Murine Thrombin.


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Structure of Human Thrombin with Residues 145-150 of Murine Thrombin. within 5.0Å range: probe atom residue distance (Å) B Occ B:Na402 b:34.2 occ:1.00 O A:HOH219 2.3 32.2 1.0 OH B:TYR134 2.4 29.3 1.0 O A:HOH165 2.4 41.9 0.5 O A:TYR14J 2.6 29.2 1.0 CZ B:TYR134 3.3 25.8 1.0 C A:TYR14J 3.6 28.8 1.0 CE1 B:TYR134 3.6 26.7 1.0 N A:ILE14K 4.4 31.1 1.0 CE2 B:TYR134 4.5 23.8 1.0 CA A:TYR14J 4.5 25.6 1.0 O A:ASP14L 4.5 46.5 1.0 O B:HOH340 4.5 31.1 1.0 C A:ILE14K 4.5 37.9 1.0 CA A:ILE14K 4.6 35.0 1.0 O A:ILE14K 4.6 39.2 1.0 C A:ASP14L 4.7 44.3 1.0 O A:SER14I 4.8 25.3 1.0 CD1 B:TYR134 4.9 23.9 1.0 N A:ASP14L 4.9 39.5 1.0

N.Pozzi, R.Chen, Z.Chen, A.Bah, E.Di Cera. Rigidification of the Autolysis Loop Enhances Na(+) Binding to Thrombin. Biophys.Chem. V. 159 6 2011.
ISSN: ISSN 0301-4622
PubMed: 21536369
DOI: 10.1016/J.BPC.2011.04.003