Sodium in PDB 3jz1: Crystal Structure of Human Thrombin Mutant N143P in E:Na+ Form

All present enzymatic activity of Crystal Structure of Human Thrombin Mutant N143P in E:Na+ Form:
3.4.21.5;

The structure of Crystal Structure of Human Thrombin Mutant N143P in E:Na+ Form, PDB code: 3jz1 was solved by W.Niu, Z.Chen, L.A.Bush-Pelc, A.Bah, P.S.Gandhi, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	26.57 / 1.60
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	119.979, 47.670, 50.688, 90.00, 92.29, 90.00
R / Rfree (%)	20.3 / 21.6

The binding sites of Sodium atom in the Crystal Structure of Human Thrombin Mutant N143P in E:Na+ Form (pdb code 3jz1). 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 N143P in E:Na+ Form, PDB code: 3jz1:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of Human Thrombin Mutant N143P in E:Na+ Form


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 N143P in E:Na+ Form within 5.0Å range: probe atom residue distance (Å) B Occ A:Na402 b:21.3 occ:1.00 O A:TYR14J 2.3 20.1 1.0 OH B:TYR134 2.3 20.3 1.0 O3 A:NO3404 2.4 59.6 0.5 O A:HOH1132 2.4 24.5 1.0 N A:NO3404 2.5 52.9 0.5 O1 A:NO3404 2.8 59.3 0.5 CZ B:TYR134 3.2 18.3 1.0 O2 A:NO3404 3.2 53.4 0.5 C A:TYR14J 3.4 17.3 1.0 CE1 B:TYR134 3.6 19.8 1.0 O A:ASP14L 4.0 45.9 1.0 CA A:TYR14J 4.3 16.8 1.0 N A:ILE14K 4.3 18.8 1.0 CE2 B:TYR134 4.3 20.1 1.0 CA A:ILE14K 4.3 23.6 1.0 C A:ILE14K 4.5 26.6 1.0 O B:HOH1011 4.6 22.7 1.0 O A:SER14I 4.7 20.5 1.0 N A:ASP14L 4.8 31.7 1.0 CD1 B:TYR134 4.8 16.7 1.0 O A:ILE14K 4.9 26.8 1.0 C A:ASP14L 4.9 44.8 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of Human Thrombin Mutant N143P in E:Na+ Form


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 N143P in E:Na+ Form within 5.0Å range: probe atom residue distance (Å) B Occ B:Na401 b:28.0 occ:1.00 O B:HOH1131 2.1 27.7 1.0 O B:LYS224 2.3 23.9 1.0 O B:HOH1124 2.4 26.4 1.0 O B:HOH1138 2.4 33.3 1.0 O B:ARG221A 2.4 32.5 1.0 O B:HOH1119 2.9 36.5 1.0 C B:LYS224 3.4 23.7 1.0 C B:ARG221A 3.4 37.7 1.0 N B:LYS224 3.8 25.4 1.0 N B:ARG221A 3.8 31.4 1.0 O B:HOH1045 4.0 28.8 1.0 O B:HOH1013 4.0 35.6 1.0 CA B:LYS224 4.1 25.9 1.0 O B:TYR184A 4.1 24.7 1.0 C B:ASP221 4.1 33.6 1.0 CA B:ARG221A 4.3 36.2 1.0 N B:ASP222 4.3 33.7 1.0 O B:HOH1093 4.3 25.6 1.0 N B:GLY223 4.3 29.4 1.0 CA B:ASP221 4.4 35.0 1.0 CA B:ASP222 4.4 31.4 1.0 CB B:LYS224 4.4 23.0 1.0 O B:HOH1189 4.4 47.4 1.0 N B:TYR225 4.4 22.6 1.0 C B:ASP222 4.6 29.3 1.0 OD1 B:ASP221 4.6 33.8 1.0 CA B:TYR225 4.7 21.1 1.0 O B:ASP221 4.7 33.2 1.0 C B:GLY223 4.8 24.8 1.0 CD1 B:TYR225 5.0 21.2 1.0

W.Niu, Z.Chen, L.A.Bush-Pelc, A.Bah, P.S.Gandhi, E.Di Cera. Mutant N143P Reveals How Na+ Activates Thrombin J.Biol.Chem. V. 284 36175 2009.
ISSN: ISSN 0021-9258
PubMed: 19846563
DOI: 10.1074/JBC.M109.069500