Chlorine in PDB 6yhj: Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E):
3.4.21.5;

The structure of Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E), PDB code: 6yhj was solved by A.Sandner, A.Heine, G.Klebe, C.Collins, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.53 / 1.44
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.285, 71.399, 72.56, 90, 100.58, 90
R / Rfree (%)	12.7 / 15.4

The structure of Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E) also contains other interesting chemical elements:

Sodium

(Na)

2 atoms

The binding sites of Chlorine atom in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E) (pdb code 6yhj). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E), PDB code: 6yhj:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)


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 D-Phe-Pro-2-Chlorothiophen Derivative (16E) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl305 b:29.5 occ:0.85 CL H:OQZ305 0.0 29.5 0.8 C8 H:OQZ305 1.7 29.2 0.8 HA H:PHE232 2.5 14.7 1.0 O H:PRO124 2.6 18.7 1.0 C7 H:OQZ305 2.7 27.2 0.8 HD2 H:PRO124 2.9 16.6 1.0 HG2 H:PRO124 3.0 18.5 1.0 S H:OQZ305 3.0 32.2 0.8 HD1 H:PHE232 3.0 20.2 1.0 HG12 H:VAL231 3.0 14.6 1.0 HB3 H:LEU123 3.2 16.3 1.0 HB2 H:LYS235 3.3 25.2 1.0 CA H:PHE232 3.4 12.2 1.0 HB2 H:PHE232 3.4 15.3 1.0 CD H:PRO124 3.5 13.8 1.0 N H:PRO124 3.5 13.1 1.0 CG H:PRO124 3.6 15.4 1.0 C H:PRO124 3.6 17.3 1.0 N H:PHE232 3.8 11.7 1.0 CD1 H:PHE232 3.9 16.8 1.0 CB H:PHE232 3.9 12.8 1.0 C6 H:OQZ305 3.9 26.9 0.8 CG1 H:VAL231 4.0 12.2 1.0 HD2 H:LYS235 4.0 32.8 1.0 C H:LEU123 4.0 13.2 1.0 CB H:LEU123 4.1 13.6 1.0 CA H:PRO124 4.1 14.9 1.0 C5 H:OQZ305 4.1 27.1 0.8 O H:VAL231 4.1 12.3 1.0 C H:VAL231 4.1 10.6 1.0 H H:PHE232 4.2 14.1 1.0 CB H:LYS235 4.2 21.0 1.0 HG11 H:VAL231 4.3 14.6 1.0 HB2 H:LEU123 4.3 16.3 1.0 HG3 H:PRO124 4.4 18.5 1.0 HG3 H:LYS235 4.4 29.3 1.0 CG H:PHE232 4.4 16.0 1.0 HD3 H:PRO124 4.4 16.6 1.0 HG13 H:VAL231 4.4 14.6 1.0 CB H:PRO124 4.4 15.4 1.0 HA H:LYS235 4.5 23.0 1.0 C H:PHE232 4.5 13.0 1.0 HD13 H:LEU123 4.5 20.2 1.0 CA H:LEU123 4.5 12.9 1.0 HA H:ASP125 4.6 22.6 0.4 O H:PHE232 4.6 14.4 1.0 HA H:LEU123 4.6 15.5 1.0 O H:LEU123 4.7 14.5 1.0 HB2 H:PRO124 4.7 18.5 1.0 CG H:LYS235 4.7 24.4 1.0 HB H:VAL231 4.7 13.2 1.0 HB3 H:PHE232 4.8 15.3 1.0 CD H:LYS235 4.8 27.3 1.0 N H:ASP125 4.8 17.9 0.4 N H:ASP125 4.8 18.1 0.6 HB3 H:LYS235 4.8 25.2 1.0 HD12 H:ILE238 4.9 20.4 1.0 CA H:LYS235 4.9 19.1 1.0 CB H:VAL231 4.9 11.0 1.0 CE1 H:PHE232 4.9 19.1 1.0 HA H:ASP125 5.0 23.0 0.6 HA H:PRO124 5.0 17.9 1.0 HD22 H:LEU123 5.0 18.6 1.0 HE1 H:PHE232 5.0 22.9 1.0

Chlorine binding site 2 out of 2 in the Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E)


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 D-Phe-Pro-2-Chlorothiophen Derivative (16E) within 5.0Å range: probe atom residue distance (Å) B Occ H:Cl306 b:37.9 occ:1.00 CL H:OQZ306 0.0 37.9 1.0 C8 H:OQZ306 1.7 34.9 1.0 C7 H:OQZ306 2.7 31.3 1.0 HB3 H:ALA190 2.8 19.6 1.0 S H:OQZ306 3.0 36.0 1.0 HA2 H:GLY226 3.0 15.5 1.0 HA3 H:GLY226 3.1 15.5 1.0 O H:HOH402 3.1 35.0 1.0 OD1 H:ASP189 3.2 16.8 1.0 HA3 H:GLY216 3.3 16.8 1.0 CA H:GLY226 3.5 12.9 1.0 O H:TRP215 3.6 13.0 1.0 CB H:ALA190 3.7 16.4 1.0 H H:PHE227 3.8 13.1 1.0 O H:ALA190 3.8 18.5 1.0 H H:ALA190 3.8 18.4 1.0 C6 H:OQZ306 3.9 30.1 1.0 CG H:ASP189 4.0 17.2 1.0 C H:TRP215 4.0 12.1 1.0 HB1 H:ALA190 4.0 19.6 1.0 C H:ALA190 4.1 17.5 1.0 CA H:GLY216 4.1 14.0 1.0 OD2 H:ASP189 4.1 18.5 1.0 HG13 H:VAL213 4.1 14.9 1.0 C5 H:OQZ306 4.1 27.4 1.0 N H:GLY216 4.2 12.8 1.0 CA H:ALA190 4.3 16.0 1.0 HB2 H:ALA190 4.3 19.6 1.0 N H:ALA190 4.3 15.3 1.0 N H:PHE227 4.4 10.9 1.0 HA2 H:GLY216 4.5 16.8 1.0 C H:GLY226 4.5 11.5 1.0 N H:GLY226 4.5 13.0 1.0 O H:HOH470 4.7 14.4 1.0 H H:GLY216 4.7 15.4 1.0 HA H:CYS191 4.7 23.3 1.0 N H:CYS191 4.8 17.9 1.0 H H:TRP215 4.8 14.1 1.0 H H:GLY226 4.9 15.6 1.0 CG1 H:VAL213 4.9 12.5 1.0 HA H:TRP215 4.9 14.2 1.0 CA H:TRP215 5.0 11.8 1.0 HG11 H:VAL213 5.0 14.9 1.0

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-2-Chlorothiophen Derivative (16E) To Be Published.