Sodium in PDB 3utu: High Affinity Inhibitor of Human Thrombin

All present enzymatic activity of High Affinity Inhibitor of Human Thrombin:
3.4.21.5;

The structure of High Affinity Inhibitor of Human Thrombin, PDB code: 3utu was solved by B.Baum, T.Steinmetzer, 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 / 1.55
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.770, 71.350, 72.390, 90.00, 100.65, 90.00
R / Rfree (%)	21.7 / 29.5

The structure of High Affinity Inhibitor of Human Thrombin also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

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

Sodium binding site 1 out of 2 in the High Affinity Inhibitor of Human Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of High Affinity Inhibitor of Human Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na902 b:19.3 occ:1.00 O H:ARG221A 2.3 19.3 1.0 O H:HOH1098 2.3 20.0 1.0 O H:HOH1144 2.4 19.5 1.0 O H:LYS224 2.5 16.3 1.0 O H:HOH1033 2.5 14.9 1.0 O H:HOH1055 2.7 17.9 1.0 C H:ARG221A 3.4 17.5 1.0 C H:LYS224 3.5 15.8 1.0 N H:LYS224 3.8 15.4 1.0 O H:HOH1030 3.9 16.8 1.0 O H:HOH1074 3.9 22.3 1.0 N H:ARG221A 3.9 17.0 1.0 O H:TYR184A 4.1 19.2 1.0 CA H:LYS224 4.1 11.8 1.0 N H:ASP222 4.2 18.1 1.0 C H:ASP221 4.2 21.3 1.0 CA H:ASP222 4.3 18.8 1.0 N H:GLY223 4.3 26.3 1.0 CA H:ARG221A 4.3 20.4 1.0 CA H:ASP221 4.3 19.5 1.0 O H:HOH1095 4.4 16.7 1.0 C H:ASP222 4.4 21.1 1.0 CB H:LYS224 4.5 13.9 1.0 N H:TYR225 4.5 19.6 1.0 OD1 H:ASP221 4.6 19.1 1.0 C H:GLY223 4.7 22.2 1.0 CA H:TYR225 4.8 20.5 1.0 O H:HOH1046 4.8 20.5 1.0 O H:ASP221 4.8 33.1 1.0

Sodium binding site 2 out of 2 in the High Affinity Inhibitor of Human Thrombin


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of High Affinity Inhibitor of Human Thrombin within 5.0Å range: probe atom residue distance (Å) B Occ H:Na903 b:13.1 occ:1.00 O H:LYS169 2.3 20.1 1.0 O H:THR172 2.3 14.4 1.0 O H:HOH1034 2.4 16.8 1.0 O H:HOH1048 2.4 21.1 1.0 C H:LYS169 3.4 17.3 1.0 C H:THR172 3.6 14.0 1.0 CA H:ASP170 4.0 16.8 1.0 N H:ASP170 4.1 19.8 1.0 N H:THR172 4.3 13.7 1.0 C H:ASP170 4.3 16.6 1.0 CA H:ARG173 4.4 20.8 1.0 CA H:LYS169 4.4 14.4 1.0 N H:ARG173 4.5 16.2 1.0 CA H:THR172 4.5 18.0 1.0 OD1 H:ASP170 4.6 18.9 1.0 CG2 H:THR172 4.7 18.7 1.0 CB H:LYS169 4.7 21.2 1.0 O H:ASP170 4.8 16.7 1.0 N H:SER171 4.8 14.2 1.0 C H:ARG173 4.9 19.3 1.0

T.Steinmetzer, B.Baum, A.Biela, G.Klebe, G.Nowak, E.Bucha. Beyond Heparinization: Design of Highly Potent Thrombin Inhibitors Suitable For Surface Coupling Chemmedchem V. 7 1965 2012.
ISSN: ISSN 1860-7179
PubMed: 22907907
DOI: 10.1002/CMDC.201200292