Sodium in PDB 2zhw: Exploring Thrombin S3 Pocket

All present enzymatic activity of Exploring Thrombin S3 Pocket:
3.4.21.5;

The structure of Exploring Thrombin S3 Pocket, PDB code: 2zhw was solved by T.Brandt, B.Baum, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	10.00 / 2.02
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	68.900, 71.500, 71.300, 90.00, 99.10, 90.00
R / Rfree (%)	20.2 / 29.2

The binding sites of Sodium atom in the Exploring Thrombin S3 Pocket (pdb code 2zhw). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Exploring Thrombin S3 Pocket, PDB code: 2zhw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Exploring Thrombin S3 Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Exploring Thrombin S3 Pocket within 5.0Å range: probe atom residue distance (Å) B Occ H:Na601 b:33.6 occ:1.00 O H:THR172 2.1 29.9 1.0 O H:LYS169 2.3 37.5 1.0 C H:THR172 3.4 27.9 1.0 C H:LYS169 3.5 29.2 1.0 CA H:ASP170 4.2 27.4 1.0 N H:THR172 4.2 30.2 1.0 N H:ARG173 4.2 26.8 1.0 N H:ASP170 4.3 33.1 1.0 CA H:ARG173 4.3 36.8 1.0 CA H:THR172 4.4 30.3 1.0 CA H:LYS169 4.5 35.6 1.0 C H:ASP170 4.5 29.9 1.0 CG2 H:THR172 4.7 24.7 1.0 C H:ARG173 4.8 38.5 1.0 N H:SER171 4.9 27.4 1.0 O H:ILE174 4.9 41.0 1.0 O H:ASP170 4.9 41.7 1.0 OD1 H:ASP170 4.9 23.3 1.0 CB H:LYS169 5.0 35.1 1.0

Sodium binding site 2 out of 2 in the Exploring Thrombin S3 Pocket


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Exploring Thrombin S3 Pocket within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:51.8 occ:1.00 O H:LYS224 2.5 45.9 1.0 O H:ARG221A 2.7 35.3 1.0 O H:HOH1085 2.8 29.5 1.0 O H:HOH1045 3.0 28.9 1.0 N H:ARG221A 3.2 47.1 1.0 C H:ARG221A 3.4 40.3 1.0 C H:LYS224 3.5 41.9 1.0 C H:ASP221 3.6 53.8 1.0 CA H:ASP221 3.6 43.3 1.0 CA H:ARG221A 3.9 39.1 1.0 OD1 H:ASP221 4.2 31.4 1.0 CA H:LYS224 4.3 36.1 1.0 N H:ASP221 4.3 41.1 1.0 N H:LYS224 4.3 33.5 1.0 N H:TYR225 4.3 41.1 1.0 OD2 H:ASP189 4.4 23.4 1.0 CB H:LYS224 4.4 35.4 1.0 N H:ASP222 4.4 46.5 1.0 O H:ASP221 4.5 64.1 1.0 O H:HOH1101 4.5 36.6 1.0 CA H:TYR225 4.6 36.0 1.0 O H:HOH1037 4.6 40.1 1.0 CG H:ASP189 4.8 32.2 1.0 CA H:ASP222 4.8 40.5 1.0 CB H:ASP221 4.8 27.1 1.0 CB H:ASP189 4.8 36.2 1.0 CB H:ARG221A 4.9 37.3 1.0 CG H:ASP221 4.9 24.9 1.0 O H:GLY188 4.9 29.5 1.0

T.Brandt, B.Baum, D.Hangauer, A.Heine, G.Klebe. Exploring Thrombin S3 Pocket To Be Published.