Sodium in PDB 2znk: Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

The structure of Thrombin Inhibition, PDB code: 2znk 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 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.200, 71.600, 72.500, 90.00, 100.50, 90.00
R / Rfree (%)	18 / 22.9

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

Sodium binding site 1 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na3002 b:15.6 occ:1.00 O H:HOH4183 2.2 17.8 1.0 O H:HOH4042 2.3 15.1 1.0 O H:LYS224 2.3 13.9 1.0 O H:HOH4054 2.4 10.8 1.0 O H:ARG221A 2.4 14.9 1.0 O H:HOH4112 2.7 23.3 1.0 C H:LYS224 3.4 9.0 1.0 C H:ARG221A 3.5 17.7 1.0 O H:HOH4057 3.8 21.9 1.0 O H:HOH4037 3.9 14.2 1.0 N H:ARG221A 3.9 19.1 1.0 N H:LYS224 4.0 10.9 1.0 O H:TYR184A 4.0 16.2 1.0 C H:ASP221 4.1 15.9 1.0 O H:HOH4022 4.1 12.1 1.0 CA H:LYS224 4.2 8.1 1.0 N H:ASP222 4.3 16.4 1.0 CA H:ARG221A 4.3 20.2 1.0 CA H:ASP221 4.3 16.4 1.0 CA H:ASP222 4.3 20.6 1.0 N H:GLY223 4.4 20.3 1.0 N H:TYR225 4.4 14.2 1.0 O H:HOH4043 4.5 22.5 1.0 C H:ASP222 4.6 21.2 1.0 O H:ASP221 4.6 20.4 1.0 CB H:LYS224 4.6 12.7 1.0 OD1 H:ASP221 4.7 21.6 1.0 CA H:TYR225 4.8 13.7 1.0 C H:GLY223 4.9 15.8 1.0

Sodium binding site 2 out of 2 in the Thrombin Inhibition


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin Inhibition within 5.0Å range: probe atom residue distance (Å) B Occ H:Na3003 b:12.8 occ:1.00 O H:THR172 2.3 9.9 1.0 O H:LYS169 2.4 16.0 1.0 O H:HOH4065 2.4 17.7 1.0 O H:HOH4049 2.4 13.2 1.0 O H:HOH4028 2.5 16.7 1.0 C H:LYS169 3.5 15.0 1.0 C H:THR172 3.5 6.9 1.0 CA H:ASP170 4.0 11.7 1.0 N H:ASP170 4.2 17.0 1.0 N H:THR172 4.3 14.6 1.0 N H:ARG173 4.3 8.8 1.0 CA H:ARG173 4.4 16.4 1.0 C H:ASP170 4.4 13.4 1.0 O H:HOH4141 4.4 28.1 1.0 CA H:THR172 4.5 11.3 1.0 CA H:LYS169 4.5 11.0 1.0 OD1 H:ASP170 4.7 14.0 1.0 CG2 H:THR172 4.8 9.7 1.0 N H:SER171 4.8 9.1 1.0 O H:ASP170 4.8 14.1 1.0 C H:ARG173 4.9 17.1 1.0 O H:HOH4061 4.9 21.8 1.0 CB H:LYS169 4.9 13.8 1.0 O H:ILE174 5.0 14.4 1.0

B.Baum, L.Muley, M.Smolinski, A.Heine, D.Hangauer, G.Klebe. Non-Additivity of Functional Group Contributions in Protein-Ligand Binding: A Comprehensive Study By Crystallography and Isothermal Titration Calorimetry. J.Mol.Biol. V. 397 1042 2010.
ISSN: ISSN 0022-2836
PubMed: 20156458
DOI: 10.1016/J.JMB.2010.02.007