Sodium in PDB 2zhe: 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: 2zhe 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 / 2.10
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.400, 71.200, 72.400, 90.00, 100.40, 90.00
R / Rfree (%)	20.6 / 29.8

The binding sites of Sodium atom in the Exploring Thrombin S3 Pocket (pdb code 2zhe). 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: 2zhe:
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:25.4 occ:1.00 O H:THR172 2.3 21.8 1.0 O H:LYS169 2.4 21.3 1.0 O H:HOH1059 2.6 28.8 1.0 C H:LYS169 3.5 22.0 1.0 C H:THR172 3.6 19.6 1.0 CA H:ASP170 4.1 20.4 1.0 N H:ASP170 4.2 20.8 1.0 N H:THR172 4.3 18.0 1.0 CA H:ARG173 4.4 20.5 1.0 N H:ARG173 4.4 19.3 1.0 C H:ASP170 4.5 21.4 1.0 CA H:THR172 4.6 17.2 1.0 CA H:LYS169 4.6 24.7 1.0 O H:ASP170 4.8 18.3 1.0 CG2 H:THR172 4.8 12.4 1.0 OD1 H:ASP170 4.9 15.4 1.0 N H:SER171 4.9 19.6 1.0 CB H:LYS169 5.0 28.8 1.0 C H:ARG173 5.0 20.1 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:24.2 occ:1.00 O H:LYS224 2.3 25.9 1.0 O H:ARG221A 2.3 30.9 1.0 O H:HOH1092 2.5 25.5 1.0 O H:HOH1055 2.6 23.1 1.0 O H:HOH1083 2.8 19.7 1.0 O H:HOH1048 3.0 21.8 1.0 C H:ARG221A 3.4 31.8 1.0 C H:LYS224 3.4 24.2 1.0 O H:HOH1077 3.5 22.5 1.0 N H:LYS224 3.7 22.9 1.0 N H:ARG221A 3.8 26.6 1.0 C H:ASP221 4.0 25.7 1.0 O H:TYR184A 4.0 17.4 1.0 CA H:LYS224 4.1 23.7 1.0 O H:HOH1032 4.1 18.5 1.0 N H:GLY223 4.1 30.6 1.0 O H:HOH1038 4.2 40.5 1.0 CA H:ARG221A 4.2 30.1 1.0 CA H:ASP221 4.3 22.8 1.0 N H:ASP222 4.3 32.9 1.0 CA H:ASP222 4.4 33.4 1.0 C H:ASP222 4.4 31.7 1.0 N H:TYR225 4.4 21.5 1.0 O H:ASP221 4.5 26.7 1.0 CB H:LYS224 4.5 25.1 1.0 OD1 H:ASP221 4.6 20.7 1.0 CA H:TYR225 4.7 23.0 1.0 C H:GLY223 4.7 25.6 1.0 CA H:GLY223 4.9 28.1 1.0

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