Sodium in PDB 3rlw: Human Thrombin in Complex with MI328

All present enzymatic activity of Human Thrombin in Complex with MI328:
3.4.21.5;

The structure of Human Thrombin in Complex with MI328, PDB code: 3rlw 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)	34.65 / 1.69
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.500, 71.300, 72.500, 90.00, 100.60, 90.00
R / Rfree (%)	16.3 / 19.2

The binding sites of Sodium atom in the Human Thrombin in Complex with MI328 (pdb code 3rlw). 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 MI328, PDB code: 3rlw:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Human Thrombin in Complex with MI328


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 MI328 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na6 b:14.8 occ:1.00 O H:HOH1064 2.3 16.5 1.0 O H:THR172 2.3 16.1 1.0 O H:LYS169 2.4 19.5 1.0 O H:HOH1076 2.4 29.9 1.0 O H:HOH1062 2.5 24.4 1.0 C H:LYS169 3.5 14.3 1.0 C H:THR172 3.6 14.6 1.0 CA H:ASP170 4.1 17.0 1.0 N H:ASP170 4.2 14.8 1.0 N H:THR172 4.3 14.0 1.0 CA H:ARG173 4.4 15.4 1.0 N H:ARG173 4.4 14.9 1.0 O H:HOH1169 4.5 36.8 1.0 C H:ASP170 4.5 17.1 1.0 CA H:LYS169 4.5 12.4 1.0 CA H:THR172 4.5 15.5 1.0 CG2 H:THR172 4.7 16.7 1.0 OD1 H:ASP170 4.8 21.7 1.0 O H:ASP170 4.8 17.4 1.0 CB H:LYS169 4.9 17.6 1.0 C H:ARG173 4.9 18.4 1.0 N H:SER171 4.9 15.8 1.0 O H:ILE174 5.0 14.7 1.0

Sodium binding site 2 out of 2 in the Human Thrombin in Complex with MI328


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 MI328 within 5.0Å range: probe atom residue distance (Å) B Occ H:Na7 b:21.9 occ:1.00 O H:ARG221A 2.3 20.4 1.0 O H:HOH1167 2.4 20.8 1.0 O H:LYS224 2.4 21.1 1.0 O H:HOH1103 2.4 17.3 1.0 O H:HOH1086 2.4 22.1 1.0 O H:HOH1093 2.5 22.2 1.0 C H:ARG221A 3.4 20.8 1.0 C H:LYS224 3.5 19.3 1.0 N H:LYS224 3.8 17.9 1.0 O H:HOH1054 3.9 17.1 1.0 O H:HOH1079 3.9 23.7 1.0 N H:ARG221A 4.0 21.7 1.0 O H:TYR184A 4.0 18.6 1.0 N H:GLY223 4.1 25.9 1.0 C H:ASP221 4.2 23.0 1.0 CA H:LYS224 4.2 18.6 1.0 N H:ASP222 4.2 22.2 1.0 CA H:ASP222 4.2 24.3 1.0 O H:HOH1052 4.3 16.8 1.0 CA H:ARG221A 4.3 21.8 1.0 C H:ASP222 4.4 22.6 1.0 CA H:ASP221 4.4 20.8 1.0 N H:TYR225 4.5 17.8 1.0 CB H:LYS224 4.5 18.8 1.0 OD1 H:ASP221 4.6 20.4 1.0 O H:ASP221 4.7 24.3 1.0 CA H:TYR225 4.8 16.9 1.0 C H:GLY223 4.8 21.2 1.0 O H:HOH1120 4.8 30.0 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