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Chlorine in PDB 6yb6: Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C)

Enzymatic activity of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C)

All present enzymatic activity of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C):
3.4.21.5;

Protein crystallography data

The structure of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C), PDB code: 6yb6 was solved by A.Sandner, A.Heine, G.Klebe, N.Abazi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.59 / 1.33
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 70.436, 71.2, 72.316, 90, 100.2, 90
R / Rfree (%) 13.1 / 15.3

Other elements in 6yb6:

The structure of Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) also contains other interesting chemical elements:

Sodium (Na) 2 atoms

Chlorine Binding Sites:

The binding sites of Chlorine atom in the Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) (pdb code 6yb6). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total only one binding site of Chlorine was determined in the Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C), PDB code: 6yb6:

Chlorine binding site 1 out of 1 in 6yb6

Go back to Chlorine Binding Sites List in 6yb6
Chlorine binding site 1 out of 1 in the Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C)


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-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl102

b:40.9
occ:0.91
 CL D:OJK102 0.0 40.9 0.9
C18 D:OJK102 1.7 36.4 0.9
O H:GLY219 2.6 26.0 1.0
C19 D:OJK102 2.7 32.0 0.9
C17 D:OJK102 2.7 35.3 0.9
HA H:CYS220 2.9 24.5 1.0
HA H:CYS191 3.0 26.2 1.0
O2 D:OJK102 3.0 37.5 0.9
O H:ALA190 3.2 20.9 1.0
SG H:CYS220 3.3 24.7 1.0
O H:HOH404 3.4 43.5 1.0
C H:GLY219 3.5 22.9 1.0
O H:HOH454 3.6 26.0 1.0
CA H:CYS220 3.6 20.4 1.0
HA3 H:GLY216 3.7 19.1 1.0
CB H:CYS220 3.9 23.1 1.0
CA H:CYS191 3.9 21.8 1.0
OD2 H:ASP189 3.9 17.1 1.0
HB3 H:CYS220 3.9 27.7 1.0
N H:CYS220 3.9 21.6 1.0
C20 D:OJK102 4.0 26.9 0.9
C16 D:OJK102 4.0 31.1 0.9
C H:ALA190 4.0 18.6 1.0
N H:CYS191 4.3 19.1 1.0
C15 D:OJK102 4.5 26.1 0.9
CA H:GLY216 4.5 15.9 1.0
CG H:ASP189 4.6 15.7 1.0
C H:CYS191 4.7 24.7 1.0
H H:GLY219 4.7 25.2 1.0
CA H:GLY219 4.7 21.1 1.0
CB H:CYS191 4.7 22.5 1.0
H H:CYS220 4.7 26.0 1.0
HB3 H:ALA190 4.7 21.5 1.0
HB2 H:CYS191 4.7 27.0 1.0
N H:GLY219 4.8 21.0 1.0
C H:GLY216 4.8 17.2 1.0
H H:ASP221 4.8 21.8 1.0
HB2 H:CYS220 4.8 27.7 1.0
OD1 H:ASP189 4.8 15.3 1.0
H H:GLU192 4.8 30.9 1.0
SG H:CYS191 4.8 25.5 1.0
HA2 H:GLY219 5.0 25.4 1.0
N H:GLU192 5.0 25.7 1.0
N H:GLY216 5.0 15.0 1.0

Reference:

A.Sandner, A.Heine, G.Klebe. Thrombin in Complex with D-Phe-Pro-3-Chloro-1,3-Dihydroxybenzylamide Derivative (13C) To Be Published.
Page generated: Mon Jul 29 17:37:14 2024

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