Sodium in PDB 2zf0: 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: 2zf0 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 / 2.20
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.000, 70.300, 72.500, 90.00, 101.10, 90.00
R / Rfree (%)	17 / 26.7

The binding sites of Sodium atom in the Exploring Thrombin S1 Pocket (pdb code 2zf0). 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: 2zf0:
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:20.3 occ:1.00 O H:HOH1144 2.3 16.8 1.0 O H:LYS224 2.3 10.3 1.0 O H:ARG221A 2.4 21.1 1.0 O H:HOH1092 2.5 24.6 1.0 O H:HOH1093 3.2 22.8 1.0 C H:LYS224 3.3 18.8 1.0 C H:ARG221A 3.4 23.4 1.0 O H:HOH1043 3.8 12.3 1.0 N H:LYS224 3.8 19.8 1.0 N H:ARG221A 3.9 21.5 1.0 C H:ASP221 4.0 19.2 1.0 CA H:LYS224 4.0 17.6 1.0 O H:HOH1044 4.0 23.1 1.0 CA H:ASP221 4.1 17.7 1.0 N H:ASP222 4.2 22.9 1.0 O H:HOH1042 4.2 18.1 1.0 N H:TYR225 4.3 11.1 1.0 O H:HOH1003 4.3 6.9 1.0 CB H:LYS224 4.3 26.4 1.0 CA H:ARG221A 4.3 25.3 1.0 CA H:ASP222 4.3 15.1 1.0 O H:TYR184A 4.3 11.5 1.0 N H:GLY223 4.4 25.8 1.0 CA H:TYR225 4.5 14.8 1.0 C H:ASP222 4.5 10.3 1.0 O H:ASP221 4.5 16.2 1.0 OD1 H:ASP221 4.6 12.6 1.0 N H:ASP221 4.7 11.8 1.0 C H:GLY223 4.9 23.2 1.0 OD2 H:ASP189 5.0 19.8 1.0 CD2 H:TYR225 5.0 17.7 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:18.5 occ:1.00 O H:THR172 2.2 9.1 1.0 O H:LYS169 2.3 9.9 1.0 O H:HOH1081 2.7 23.5 1.0 C H:LYS169 3.3 9.4 1.0 C H:THR172 3.4 14.0 1.0 CA H:ASP170 4.0 15.4 1.0 N H:ASP170 4.1 11.1 1.0 N H:THR172 4.1 12.6 1.0 N H:ARG173 4.3 11.2 1.0 C H:ASP170 4.3 17.9 1.0 CA H:THR172 4.3 13.8 1.0 CA H:ARG173 4.3 18.1 1.0 CA H:LYS169 4.4 19.6 1.0 CG2 H:THR172 4.7 1.3 1.0 OD1 H:ASP170 4.7 13.2 1.0 N H:SER171 4.7 16.8 1.0 O H:ASP170 4.8 16.0 1.0 CB H:LYS169 4.8 12.4 1.0 C H:ARG173 4.9 17.0 1.0

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