Chlorine in PDB 4e7r: Thrombin in Complex with 3-Amidinophenylalanine Inhibitor

All present enzymatic activity of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor:
3.4.21.5;

The structure of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor, PDB code: 4e7r was solved by E.Ruehmann, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	29.26 / 2.25
Space group	P 1
Cell size a, b, c (Å), α, β, γ (°)	50.242, 50.284, 71.837, 97.61, 96.61, 90.57
R / Rfree (%)	17.1 / 22.3

The structure of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor also contains other interesting chemical elements:

Sodium

(Na)

4 atoms

The binding sites of Chlorine atom in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor (pdb code 4e7r). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor, PDB code: 4e7r:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:29.4 occ:1.00 CL2 H:0NW302 0.0 29.4 1.0 C37 H:0NW302 1.8 28.1 1.0 C36 H:0NW302 2.7 31.0 1.0 C38 H:0NW302 2.8 28.1 1.0 O H:ASN98 3.2 16.6 1.0 C H:ASN98 3.3 26.8 1.0 CA H:ASN98 3.5 24.3 1.0 CG H:LEU99 3.8 28.8 1.0 CE2 H:TRP215 3.8 25.7 1.0 CD2 H:TRP215 3.8 25.6 1.0 NE1 H:TRP215 3.9 20.3 1.0 N H:LEU99 4.0 23.6 1.0 CG H:TRP215 4.0 24.4 1.0 C35 H:0NW302 4.0 39.9 1.0 CD1 H:TRP215 4.1 32.5 1.0 CG2 H:ILE174 4.1 17.9 1.0 C39 H:0NW302 4.1 34.8 1.0 CB H:LEU99 4.1 20.6 1.0 CD1 H:LEU99 4.1 30.0 1.0 CZ2 H:TRP215 4.3 26.4 1.0 CB H:ASN98 4.3 18.4 1.0 O H:GLU97A 4.3 41.5 1.0 CE3 H:TRP215 4.4 29.0 1.0 CG1 H:ILE174 4.5 28.6 1.0 C34 H:0NW302 4.6 30.9 1.0 CD1 H:ILE174 4.6 28.0 1.0 N H:ASN98 4.7 29.5 1.0 CA H:LEU99 4.7 28.2 1.0 CH2 H:TRP215 4.7 30.1 1.0 CZ3 H:TRP215 4.8 30.2 1.0 CB H:TRP215 4.8 18.1 1.0 CB H:ILE174 4.9 22.8 1.0 C H:GLU97A 4.9 34.0 1.0

Chlorine binding site 2 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl302 b:48.2 occ:1.00 CL1 H:0NW302 0.0 48.2 1.0 C35 H:0NW302 1.8 39.9 1.0 C36 H:0NW302 2.7 31.0 1.0 C34 H:0NW302 2.8 30.9 1.0 C33 H:0NW302 3.1 19.6 1.0 C32 H:0NW302 3.1 31.8 1.0 CG H:GLU217 3.7 40.3 1.0 O H:GLY216 3.7 25.4 1.0 C37 H:0NW302 4.0 28.1 1.0 C39 H:0NW302 4.1 34.8 1.0 CE3 H:TRP215 4.1 29.0 1.0 C28 H:0NW302 4.2 35.5 1.0 C H:GLY216 4.2 28.1 1.0 CA H:GLU217 4.3 28.2 1.0 C31 H:0NW302 4.3 40.7 1.0 N H:GLU217 4.4 24.2 1.0 O27 H:0NW302 4.5 22.1 1.0 CZ3 H:TRP215 4.5 30.2 1.0 CB H:GLU217 4.5 29.9 1.0 C38 H:0NW302 4.5 28.1 1.0 CD H:GLU217 4.9 52.9 1.0 S25 H:0NW302 4.9 38.1 1.0 O10 H:0NW302 5.0 23.0 1.0

Chlorine binding site 3 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl1302 b:30.4 occ:1.00 CL2 G:0NW1302 0.0 30.4 1.0 C37 G:0NW1302 1.8 24.4 1.0 C36 G:0NW1302 2.7 27.7 1.0 C38 G:0NW1302 2.8 27.6 1.0 O G:ASN1098 3.3 18.8 1.0 C G:ASN1098 3.3 22.5 1.0 CA G:ASN1098 3.5 19.4 1.0 CE2 G:TRP1215 3.7 24.1 1.0 CD2 G:TRP1215 3.8 24.4 1.0 CG G:LEU1099 3.8 32.6 1.0 NE1 G:TRP1215 3.9 26.9 1.0 CG G:TRP1215 4.0 28.2 1.0 N G:LEU1099 4.0 29.0 1.0 CG2 G:ILE1174 4.0 18.5 1.0 C35 G:0NW1302 4.0 31.8 1.0 CD1 G:TRP1215 4.0 35.1 1.0 C39 G:0NW1302 4.1 25.9 1.0 CB G:LEU1099 4.1 14.9 1.0 CD1 G:LEU1099 4.2 26.0 1.0 CZ2 G:TRP1215 4.2 27.7 1.0 O G:GLU1097A 4.3 42.3 1.0 CB G:ASN1098 4.3 18.4 1.0 CE3 G:TRP1215 4.3 30.0 1.0 CG1 G:ILE1174 4.4 35.0 1.0 C34 G:0NW1302 4.6 28.9 1.0 CD1 G:ILE1174 4.6 29.7 1.0 N G:ASN1098 4.7 29.4 1.0 CA G:LEU1099 4.7 26.4 1.0 CH2 G:TRP1215 4.7 31.8 1.0 CZ3 G:TRP1215 4.7 33.2 1.0 CB G:TRP1215 4.8 16.8 1.0 CB G:ILE1174 4.9 23.8 1.0 C G:GLU1097A 4.9 30.1 1.0

Chlorine binding site 4 out of 4 in the Thrombin in Complex with 3-Amidinophenylalanine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Thrombin in Complex with 3-Amidinophenylalanine Inhibitor within 5.0Å range: probe atom residue distance (Å) B Occ G:Cl1302 b:64.8 occ:1.00 CL1 G:0NW1302 0.0 64.8 1.0 C35 G:0NW1302 1.8 31.8 1.0 C36 G:0NW1302 2.7 27.7 1.0 C34 G:0NW1302 2.8 28.9 1.0 C33 G:0NW1302 3.1 27.3 1.0 C32 G:0NW1302 3.2 33.7 1.0 CG G:GLU1217 3.5 42.1 1.0 O G:GLY1216 3.6 24.1 1.0 C37 G:0NW1302 4.0 24.4 1.0 CE3 G:TRP1215 4.0 30.0 1.0 C39 G:0NW1302 4.1 25.9 1.0 C G:GLY1216 4.1 28.7 1.0 CA G:GLU1217 4.2 29.0 1.0 C28 G:0NW1302 4.2 38.0 1.0 N G:GLU1217 4.3 24.9 1.0 C31 G:0NW1302 4.3 27.5 1.0 CZ3 G:TRP1215 4.4 33.2 1.0 CB G:GLU1217 4.4 31.3 1.0 C38 G:0NW1302 4.6 27.6 1.0 O27 G:0NW1302 4.6 18.2 1.0 CD G:GLU1217 4.7 55.9 1.0 O10 G:0NW1302 4.9 21.5 1.0 S25 G:0NW1302 4.9 36.6 1.0

M.Hammami, E.Ruehmann, M.Mauerer, A.Heine, M.Guetschow, G.Klebe, T.Steinmetzer. New 3-Amidinophenylalanine-Derived Inhibitors of Matriptase Medchemcomm V. 3 807 2012.
ISSN: ISSN 2040-2503
DOI: 10.1039/C2MD20074K