Sodium in PDB 2zc9: Thrombin in Complex with Inhibitor

All present enzymatic activity of Thrombin in Complex with Inhibitor:
3.4.21.5;

The structure of Thrombin in Complex with Inhibitor, PDB code: 2zc9 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 / 1.58
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.400, 71.300, 72.900, 90.00, 100.70, 90.00
R / Rfree (%)	18.8 / 23.3

The structure of Thrombin in Complex with Inhibitor also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Thrombin in Complex with Inhibitor (pdb code 2zc9). 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 in Complex with Inhibitor, PDB code: 2zc9:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1601 b:17.8 occ:1.00 O H:HOH2117 2.3 18.7 1.0 O H:LYS224 2.3 16.4 1.0 O H:ARG221A 2.3 20.7 1.0 O H:HOH2078 2.5 18.4 1.0 O H:HOH2063 2.5 15.0 1.0 O H:HOH2046 2.8 23.3 1.0 C H:LYS224 3.3 13.0 1.0 C H:ARG221A 3.3 26.0 1.0 O H:HOH2026 3.8 16.3 1.0 N H:LYS224 3.8 16.9 1.0 N H:ARG221A 3.9 16.4 1.0 CA H:LYS224 4.0 13.0 1.0 C H:ASP221 4.1 20.6 1.0 N H:ASP222 4.2 19.9 1.0 O H:HOH2116 4.2 14.3 1.0 O H:HOH2040 4.2 23.4 1.0 CA H:ARG221A 4.2 23.4 1.0 N H:GLY223 4.3 20.4 1.0 O H:TYR184A 4.3 19.9 1.0 CA H:ASP222 4.3 20.4 1.0 N H:TYR225 4.3 15.5 1.0 CA H:ASP221 4.4 14.4 1.0 CB H:LYS224 4.4 17.1 1.0 C H:ASP222 4.5 17.8 1.0 O H:ASP221 4.6 19.6 1.0 CA H:TYR225 4.6 15.3 1.0 OD1 H:ASP221 4.7 23.8 1.0 O H:HOH2019 4.8 20.2 1.0 C H:GLY223 4.9 18.8 1.0 CD2 H:TYR225 5.0 13.1 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with Inhibitor


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Na1602 b:12.2 occ:1.00 O H:LYS169 2.3 14.5 1.0 O H:THR172 2.4 14.4 1.0 O H:HOH2033 2.5 18.5 1.0 O H:HOH2077 2.5 25.6 1.0 O H:HOH2190 2.9 20.7 1.0 C H:LYS169 3.4 14.2 1.0 C H:THR172 3.6 16.6 1.0 CA H:ASP170 3.9 15.3 1.0 N H:ASP170 4.1 14.3 1.0 N H:THR172 4.2 13.0 1.0 C H:ASP170 4.3 18.0 1.0 O H:HOH2175 4.4 33.4 1.0 CA H:ARG173 4.4 16.7 1.0 CA H:LYS169 4.5 14.0 1.0 N H:ARG173 4.5 13.8 1.0 CA H:THR172 4.5 14.0 1.0 OD1 H:ASP170 4.6 14.9 1.0 O H:ASP170 4.7 15.1 1.0 N H:SER171 4.8 11.9 1.0 CG2 H:THR172 4.8 13.0 1.0 CB H:LYS169 4.9 11.1 1.0

B.Baum, L.Muley, A.Heine, M.Smolinski, D.Hangauer, G.Klebe. Think Twice: Understanding the High Potency of Bis(Phenyl)Methane Inhibitors of Thrombin J.Mol.Biol. V. 391 552 2009.
ISSN: ISSN 0022-2836
PubMed: 19520086
DOI: 10.1016/J.JMB.2009.06.016