Sodium in PDB 1sg8: Crystal Structure of the Procoagulant Fast Form of Thrombin

All present enzymatic activity of Crystal Structure of the Procoagulant Fast Form of Thrombin:
3.4.21.5;

The structure of Crystal Structure of the Procoagulant Fast Form of Thrombin, PDB code: 1sg8 was solved by A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, E.Di Cera, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.64 / 2.30
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	59.490, 65.580, 162.440, 90.00, 90.00, 90.00
R / Rfree (%)	21.9 / 28.9

The binding sites of Sodium atom in the Crystal Structure of the Procoagulant Fast Form of Thrombin (pdb code 1sg8). 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 the Procoagulant Fast Form of Thrombin, PDB code: 1sg8:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Procoagulant Fast Form of Thrombin


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 the Procoagulant Fast Form of Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1701 b:54.3 occ:1.00 O B:LYS224 2.5 49.8 1.0 O B:ARG221A 2.5 53.2 1.0 O B:HOH549 2.5 45.7 1.0 O B:HOH749 2.7 50.1 1.0 O B:HOH913 2.8 74.8 1.0 O B:HOH766 2.9 50.5 1.0 C B:LYS224 3.5 51.8 1.0 C B:ARG221A 3.6 51.5 1.0 O B:TYR184A 3.9 39.6 1.0 N B:LYS224 4.0 49.3 1.0 O B:HOH542 4.0 47.7 1.0 O B:HOH540 4.1 39.1 1.0 N B:ARG221A 4.2 53.2 1.0 CA B:LYS224 4.2 50.9 1.0 CA B:ASP222 4.3 50.7 1.0 C B:ASP221 4.4 54.2 1.0 N B:ASP222 4.4 50.7 1.0 N B:TYR225 4.4 49.3 1.0 CB B:LYS224 4.6 47.0 1.0 CD1 B:TYR225 4.6 54.7 1.0 N B:GLY223 4.6 52.4 1.0 CA B:ARG221A 4.6 53.4 1.0 CA B:ASP221 4.6 52.7 1.0 CA B:TYR225 4.6 50.1 1.0 CE1 B:TYR225 4.7 53.0 1.0 C B:ASP222 4.7 50.8 1.0 O B:HOH790 4.7 48.6 1.0 OD1 B:ASP221 4.9 45.8 1.0 O B:ASP221 5.0 55.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Procoagulant Fast Form of Thrombin


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 the Procoagulant Fast Form of Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ E:Na1702 b:55.0 occ:1.00 O E:HOH663 2.4 49.1 1.0 O E:HOH651 2.5 38.3 1.0 O E:ARG221A 2.5 51.0 1.0 O E:LYS224 2.5 48.6 1.0 O E:HOH649 2.5 44.4 1.0 O E:HOH664 2.9 58.2 1.0 C E:ARG221A 3.4 51.4 1.0 O E:HOH655 3.6 43.1 1.0 O E:TYR184A 3.7 47.0 1.0 O E:HOH527 3.7 49.4 1.0 C E:LYS224 3.7 50.2 1.0 N E:ARG221A 4.0 56.8 1.0 C E:ASP221 4.1 54.7 1.0 O E:HOH652 4.2 46.0 1.0 N E:ASP222 4.2 48.6 1.0 CA E:ASP222 4.3 48.4 1.0 N E:LYS224 4.3 43.9 1.0 CA E:ARG221A 4.3 51.9 1.0 O E:ASP221 4.4 55.0 1.0 CA E:ASP221 4.5 53.5 1.0 CA E:LYS224 4.6 47.7 1.0 N E:GLY223 4.6 44.5 1.0 N E:TYR225 4.6 51.4 1.0 OD1 E:ASP221 4.7 50.5 1.0 CA E:TYR225 4.7 50.9 1.0 CD1 E:TYR225 4.7 49.6 1.0 C E:ASP222 4.8 44.5 1.0 C E:TYR184A 4.8 46.0 1.0 CE1 E:TYR225 4.9 50.7 1.0 CB E:LYS224 5.0 52.5 1.0

A.O.Pineda, C.J.Carrell, L.A.Bush, S.Prasad, S.Caccia, Z.W.Chen, F.S.Mathews, E.Di Cera. Molecular Dissection of Na+ Binding to Thrombin. J.Biol.Chem. V. 279 31842 2004.
ISSN: ISSN 0021-9258
PubMed: 15152000
DOI: 10.1074/JBC.M401756200