Sodium in PDB 2zdv: Exploring Thrombin S1 Pocket

All present enzymatic activity of Exploring Thrombin S1 Pocket:
3.4.21.5;

The structure of Exploring Thrombin S1 Pocket, PDB code: 2zdv was solved by 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 / 1.72
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.500, 71.400, 72.800, 90.00, 100.60, 90.00
R / Rfree (%)	18.9 / 24.3

The structure of Exploring Thrombin S1 Pocket also contains other interesting chemical elements:

Fluorine

(F)

1 atom

The binding sites of Sodium atom in the Exploring Thrombin S1 Pocket (pdb code 2zdv). 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 S1 Pocket, PDB code: 2zdv:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Exploring Thrombin S1 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 S1 Pocket within 5.0Å range: probe atom residue distance (Å) B Occ H:Na601 b:18.0 occ:1.00 O H:HOH1127 2.2 26.1 1.0 O H:LYS224 2.3 15.2 1.0 O H:HOH1059 2.4 14.1 1.0 O H:ARG221A 2.4 19.8 1.0 O H:HOH1095 2.4 16.4 1.0 O H:HOH1093 2.8 21.2 1.0 C H:LYS224 3.4 12.6 1.0 C H:ARG221A 3.4 21.0 1.0 N H:LYS224 3.8 12.8 1.0 O H:HOH1021 3.9 21.4 1.0 N H:ARG221A 4.0 18.1 1.0 O H:HOH1063 4.1 23.7 1.0 O H:TYR184A 4.1 18.7 1.0 O H:HOH1027 4.1 14.7 1.0 CA H:LYS224 4.1 9.3 1.0 C H:ASP221 4.2 19.8 1.0 N H:GLY223 4.3 20.2 1.0 N H:ASP222 4.3 20.3 1.0 CA H:ARG221A 4.3 18.7 1.0 CA H:ASP222 4.3 23.1 1.0 N H:TYR225 4.4 13.7 1.0 CA H:ASP221 4.4 16.9 1.0 C H:ASP222 4.5 22.1 1.0 CB H:LYS224 4.6 14.3 1.0 CA H:TYR225 4.7 12.9 1.0 OD1 H:ASP221 4.8 18.3 1.0 O H:ASP221 4.8 23.3 1.0 C H:GLY223 4.9 18.4 1.0 CD2 H:TYR225 4.9 9.2 1.0

Sodium binding site 2 out of 2 in the Exploring Thrombin S1 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 S1 Pocket within 5.0Å range: probe atom residue distance (Å) B Occ H:Na602 b:10.9 occ:1.00 O H:THR172 2.3 10.4 1.0 O H:LYS169 2.3 11.7 1.0 O H:HOH1045 2.4 12.2 1.0 O H:HOH1164 2.5 25.1 1.0 O H:HOH1051 2.6 20.7 1.0 C H:LYS169 3.4 9.6 1.0 C H:THR172 3.5 10.2 1.0 CA H:ASP170 4.0 8.5 1.0 N H:ASP170 4.1 13.2 1.0 N H:THR172 4.3 12.2 1.0 N H:ARG173 4.4 12.5 1.0 C H:ASP170 4.4 13.9 1.0 CA H:ARG173 4.4 17.2 1.0 CA H:THR172 4.5 15.5 1.0 CA H:LYS169 4.5 11.0 1.0 CG2 H:THR172 4.7 13.0 1.0 OD1 H:ASP170 4.7 16.2 1.0 N H:SER171 4.8 12.4 1.0 O H:ASP170 4.8 12.4 1.0 CB H:LYS169 4.9 15.2 1.0 O H:HOH1066 5.0 21.2 1.0 C H:ARG173 5.0 12.6 1.0

B.Baum, D.Hangauer, A.Heine, G.Klebe. Exploring Thrombin S1 Pocket To Be Published.