Sodium in PDB 2zhq: Thrombin Inhibition

All present enzymatic activity of Thrombin Inhibition:
3.4.21.5;

The structure of Thrombin Inhibition, PDB code: 2zhq 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 / 1.96
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	71.100, 71.400, 72.900, 90.00, 100.80, 90.00
R / Rfree (%)	19.3 / 27.2

The binding sites of Sodium atom in the Thrombin Inhibition (pdb code 2zhq). 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: 2zhq:
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:Na601 b:1.2 occ:1.00 O H:ARG221A 2.5 13.8 1.0 O H:HOH1031 2.5 14.5 1.0 O H:HOH1153 2.5 22.8 1.0 O H:LYS224 2.5 14.9 1.0 O H:HOH1062 2.5 15.8 1.0 O H:HOH1083 2.5 22.0 1.0 C H:ARG221A 3.4 24.6 1.0 C H:LYS224 3.6 22.8 1.0 O H:HOH1050 3.7 24.1 1.0 N H:LYS224 3.8 19.0 1.0 O H:HOH1077 4.0 17.8 1.0 O H:TYR184A 4.0 23.7 1.0 CA H:ASP222 4.1 15.7 1.0 N H:ARG221A 4.1 21.3 1.0 N H:ASP222 4.1 13.3 1.0 C H:ASP221 4.2 26.4 1.0 N H:GLY223 4.2 23.0 1.0 CA H:LYS224 4.2 13.2 1.0 O H:HOH1066 4.2 11.5 1.0 CA H:ARG221A 4.4 23.2 1.0 C H:ASP222 4.4 15.4 1.0 CA H:ASP221 4.5 18.5 1.0 O H:ASP221 4.5 22.8 1.0 N H:TYR225 4.7 12.8 1.0 CB H:LYS224 4.7 14.1 1.0 C H:GLY223 4.8 19.7 1.0 OD1 H:ASP221 4.8 12.2 1.0 CA H:TYR225 4.9 10.7 1.0 CA H:GLY223 5.0 15.7 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:Na602 b:4.2 occ:1.00 O H:THR172 2.5 8.8 1.0 O H:LYS169 2.5 10.9 1.0 O H:HOH1059 2.5 17.0 1.0 O H:HOH1104 2.5 20.6 1.0 C H:LYS169 3.5 11.1 1.0 C H:THR172 3.7 9.8 1.0 CA H:ASP170 4.1 8.6 1.0 N H:ASP170 4.3 12.6 1.0 N H:THR172 4.3 7.7 1.0 C H:ASP170 4.5 14.1 1.0 CA H:ARG173 4.5 14.3 1.0 CA H:LYS169 4.6 13.6 1.0 N H:ARG173 4.6 6.8 1.0 CA H:THR172 4.6 12.2 1.0 OD1 H:ASP170 4.7 11.2 1.0 N H:SER171 4.9 16.6 1.0 O H:ASP170 4.9 9.4 1.0 CB H:LYS169 4.9 22.5 1.0 CG2 H:THR172 5.0 14.8 1.0 C H:ARG173 5.0 15.4 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