Sodium in PDB 1ype: Thrombin Inhibitor Complex

All present enzymatic activity of Thrombin Inhibitor Complex:
3.4.21.5;

The structure of Thrombin Inhibitor Complex, PDB code: 1ype was solved by J.Fokkens, U.Obst-Sander, A.Heine, F.Diederich, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 1.81
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.100, 71.400, 72.400, 90.00, 100.60, 90.00
R / Rfree (%)	17.3 / 23.5

The binding sites of Sodium atom in the Thrombin Inhibitor Complex (pdb code 1ype). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin Inhibitor Complex, PDB code: 1ype:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6666 b:15.5 occ:1.00 O H:THR172 2.3 11.9 1.0 O H:LYS169 2.4 16.1 1.0 O H:HOH9031 2.5 19.9 1.0 O H:HOH9104 2.5 21.6 1.0 C H:LYS169 3.5 18.5 1.0 C H:THR172 3.5 10.5 1.0 CA H:ASP170 4.1 13.5 1.0 N H:ASP170 4.2 16.7 1.0 N H:THR172 4.2 15.1 1.0 CA H:ARG173 4.3 17.8 1.0 N H:ARG173 4.4 16.3 1.0 C H:ASP170 4.4 13.3 1.0 CA H:THR172 4.5 11.4 1.0 CA H:LYS169 4.5 12.6 1.0 CG2 H:THR172 4.7 11.6 1.0 CG H:LYS169 4.7 41.7 1.0 OD1 H:ASP170 4.8 16.4 1.0 O H:ASP170 4.8 12.8 1.0 C H:ARG173 4.9 15.0 1.0 N H:SER171 4.9 13.6 1.0 O H:ILE174 4.9 14.6 1.0 O H:HOH9083 4.9 21.8 1.0

Sodium binding site 2 out of 2 in the Thrombin Inhibitor Complex


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibitor Complex within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6667 b:17.7 occ:1.00 O H:HOH9109 2.3 14.0 1.0 O H:ARG221A 2.4 18.4 1.0 O H:LYS224 2.4 13.0 1.0 O H:HOH9112 2.4 15.7 1.0 O H:HOH9058 2.4 15.1 1.0 O H:HOH9042 2.6 17.0 1.0 C H:ARG221A 3.4 18.7 1.0 C H:LYS224 3.5 19.6 1.0 O H:HOH9007 3.9 13.8 1.0 O H:HOH9029 3.9 14.9 1.0 N H:LYS224 3.9 14.6 1.0 N H:ARG221A 4.0 18.1 1.0 O H:TYR184A 4.0 17.2 1.0 C H:ASP221 4.1 21.3 1.0 CA H:LYS224 4.2 12.5 1.0 O H:HOH9052 4.3 13.4 1.0 N H:ASP222 4.3 16.4 1.0 CA H:ARG221A 4.3 21.0 1.0 CA H:ASP222 4.3 15.4 1.0 N H:GLY223 4.3 16.9 1.0 CA H:ASP221 4.4 20.4 1.0 N H:TYR225 4.5 14.4 1.0 O H:ASP221 4.6 18.5 1.0 C H:ASP222 4.6 14.8 1.0 OD1 H:ASP221 4.6 15.9 1.0 CB H:LYS224 4.6 11.9 1.0 O H:HOH9165 4.7 25.3 1.0 CA H:TYR225 4.8 14.2 1.0 C H:GLY223 4.9 24.1 1.0

J.Fokkens, G.Klebe. A Simple Protocol to Estimate Differences in Protein Binding Affinity For Enantiomers Without Prior Resolution of Racemates Angew.Chem.Int.Ed.Engl. V. 45 985 2006.
ISSN: ISSN 1433-7851
PubMed: 16374786
DOI: 10.1002/ANIE.200502302