Sodium in PDB 2zfr: 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: 2zfr 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 / 1.85
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.300, 71.500, 72.300, 90.00, 100.40, 90.00
R / Rfree (%)	19.3 / 25.3

The binding sites of Sodium atom in the Exploring Thrombin S3 Pocket (pdb code 2zfr). 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: 2zfr:
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:22.5 occ:1.00 O H:THR172 2.2 18.8 1.0 O H:HOH1057 2.3 21.8 1.0 O H:LYS169 2.3 23.0 1.0 O H:HOH1082 2.6 28.6 1.0 O H:HOH1040 2.6 27.6 1.0 C H:LYS169 3.4 20.6 1.0 C H:THR172 3.4 16.2 1.0 CA H:ASP170 4.1 17.3 1.0 O H:HOH1138 4.1 38.0 1.0 N H:ASP170 4.1 20.9 1.0 N H:THR172 4.2 18.5 1.0 N H:ARG173 4.3 16.7 1.0 CA H:ARG173 4.4 24.1 1.0 C H:ASP170 4.4 21.9 1.0 CA H:THR172 4.4 19.1 1.0 CA H:LYS169 4.5 18.7 1.0 OD1 H:ASP170 4.7 18.9 1.0 CG2 H:THR172 4.7 20.3 1.0 O H:ASP170 4.8 20.3 1.0 N H:SER171 4.8 18.9 1.0 CB H:LYS169 4.8 21.9 1.0 O H:ILE174 4.9 21.1 1.0 C H:ARG173 4.9 22.5 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:31.0 occ:1.00 O H:LYS224 2.3 25.2 1.0 O H:ARG221A 2.3 34.1 1.0 O H:HOH1081 2.4 21.4 1.0 O H:HOH1027 2.4 23.4 1.0 O H:HOH1074 2.7 22.1 1.0 O H:HOH1062 2.8 26.3 1.0 C H:ARG221A 3.3 31.8 1.0 C H:LYS224 3.3 20.4 1.0 N H:LYS224 3.7 19.4 1.0 O H:HOH1034 3.8 25.8 1.0 N H:ARG221A 3.8 31.1 1.0 CA H:LYS224 4.0 18.9 1.0 C H:ASP221 4.0 27.1 1.0 N H:ASP222 4.1 29.3 1.0 CA H:ARG221A 4.2 27.5 1.0 O H:TYR184A 4.2 23.8 1.0 CA H:ASP222 4.2 25.4 1.0 O H:HOH1048 4.3 27.6 1.0 O H:HOH1108 4.3 31.8 1.0 N H:GLY223 4.3 32.5 1.0 CA H:ASP221 4.3 24.6 1.0 N H:TYR225 4.3 22.1 1.0 O H:HOH1025 4.4 20.3 1.0 C H:ASP222 4.4 28.6 1.0 CB H:LYS224 4.4 24.4 1.0 O H:ASP221 4.5 29.3 1.0 OD1 H:ASP221 4.7 27.5 1.0 CA H:TYR225 4.7 22.8 1.0 C H:GLY223 4.8 30.9 1.0

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