Sodium in PDB 3rmo: Human Thrombin in Complex with MI004

All present enzymatic activity of Human Thrombin in Complex with MI004:
3.4.21.5;

The structure of Human Thrombin in Complex with MI004, PDB code: 3rmo was solved by A.Biela, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.74 / 1.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.120, 71.030, 72.750, 90.00, 100.40, 90.00
R / Rfree (%)	13.4 / 16.5

The structure of Human Thrombin in Complex with MI004 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Sodium atom in the Human Thrombin in Complex with MI004 (pdb code 3rmo). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Human Thrombin in Complex with MI004, PDB code: 3rmo:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin in Complex with MI004


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Human Thrombin in Complex with MI004 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na5 b:13.4 occ:1.00 O H:THR172 2.3 12.7 1.0 O H:LYS169 2.4 12.9 1.0 O H:HOH1138 2.4 16.5 1.0 O H:HOH1090 2.5 18.6 1.0 O H:HOH1187 2.5 18.0 1.0 C H:LYS169 3.5 12.5 1.0 C H:THR172 3.6 12.0 1.0 CA H:ASP170 4.1 11.8 1.0 CG H:LYS169 4.2 21.8 1.0 N H:ASP170 4.2 12.6 1.0 N H:THR172 4.3 11.4 1.0 CA H:ARG173 4.4 13.0 1.0 N H:ARG173 4.4 12.1 1.0 C H:ASP170 4.5 12.7 1.0 CA H:LYS169 4.5 12.2 1.0 CA H:THR172 4.5 11.8 1.0 OD1 H:ASP170 4.7 18.0 1.0 CG2 H:THR172 4.8 13.6 1.0 O H:ASP170 4.9 13.1 1.0 N H:SER171 4.9 12.1 1.0 CB H:LYS169 4.9 15.6 1.0 C H:ARG173 4.9 13.2 1.0 O H:HOH1205 5.0 24.0 1.0

Sodium binding site 2 out of 2 in the Human Thrombin in Complex with MI004


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Human Thrombin in Complex with MI004 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6 b:15.2 occ:1.00 O H:ARG221A 2.3 15.5 1.0 O H:HOH1180 2.4 15.7 1.0 O H:HOH1150 2.4 15.1 1.0 O H:LYS224 2.4 13.9 1.0 O H:HOH1097 2.4 13.5 1.0 O H:HOH1162 2.6 16.8 1.0 C H:LYS224 3.4 13.8 1.0 C H:ARG221A 3.4 15.3 1.0 N H:LYS224 3.8 15.8 1.0 O H:HOH1094 3.8 14.5 1.0 N H:ARG221A 3.9 15.6 1.0 O H:HOH1173 4.0 18.3 1.0 C H:ASP221 4.1 16.0 1.0 CA H:LYS224 4.1 14.5 1.0 O H:TYR184A 4.1 16.0 1.0 N H:GLY223 4.2 18.3 1.0 N H:ASP222 4.3 17.0 1.0 O H:HOH1164 4.3 14.7 1.0 CA H:ARG221A 4.3 16.2 1.0 CA H:ASP222 4.3 17.6 1.0 N H:TYR225 4.4 12.2 1.0 CA H:ASP221 4.4 15.7 1.0 CB H:LYS224 4.5 15.2 1.0 C H:ASP222 4.5 17.7 1.0 O H:ASP221 4.6 17.1 1.0 OD1 H:ASP221 4.6 15.5 1.0 CA H:TYR225 4.6 11.8 1.0 C H:GLY223 4.8 16.7 1.0

A.Biela, F.Sielaff, F.Terwesten, A.Heine, T.Steinmetzer, G.Klebe. Ligand Binding Stepwise Disrupts Water Network in Thrombin: Enthalpic and Entropic Changes Reveal Classical Hydrophobic Effect J.Med.Chem. V. 55 6094 2012.
ISSN: ISSN 0022-2623
PubMed: 22612268
DOI: 10.1021/JM300337Q