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Fluorine in PDB 4bs6: Mouse Cathepsin S with Covalent Ligand

Enzymatic activity of Mouse Cathepsin S with Covalent Ligand

All present enzymatic activity of Mouse Cathepsin S with Covalent Ligand:
3.4.22.27;

Protein crystallography data

The structure of Mouse Cathepsin S with Covalent Ligand, PDB code: 4bs6 was solved by D.W.Banner, J.Benz, B.Gsell, M.Stihle, A.Ruf, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 19.15 / 1.20
Space group P 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 33.270, 66.740, 97.960, 90.00, 90.36, 90.00
R / Rfree (%) 12.193 / 15.497

Other elements in 4bs6:

The structure of Mouse Cathepsin S with Covalent Ligand also contains other interesting chemical elements:

Chlorine (Cl) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Mouse Cathepsin S with Covalent Ligand (pdb code 4bs6). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Mouse Cathepsin S with Covalent Ligand, PDB code: 4bs6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4bs6

Go back to Fluorine Binding Sites List in 4bs6
Fluorine binding site 1 out of 6 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1342

b:17.7
occ:1.00
 F35 A:JG71342 0.0 17.7 1.0
C8 A:JG71342 1.3 17.4 1.0
F33 A:JG71342 2.2 16.0 1.0
F34 A:JG71342 2.2 17.8 1.0
C1 A:JG71342 2.3 15.4 1.0
HE3 A:LYS187 2.7 30.4 1.0
HA3 A:GLY191 2.7 13.7 1.0
C4 A:JG71342 2.9 14.2 1.0
O28 A:JG71342 3.1 15.3 1.0
C12 A:JG71342 3.2 16.2 1.0
H122 A:JG71342 3.2 15.8 1.0
HE2 A:LYS187 3.3 30.7 1.0
C A:GLY191 3.3 12.7 1.0
CE A:LYS187 3.3 31.6 1.0
O A:HOH2128 3.3 21.0 1.0
H A:GLY192 3.3 12.8 1.0
N A:GLY192 3.4 12.6 1.0
CA A:GLY191 3.4 13.9 1.0
HZ2 A:LYS187 3.5 32.1 1.0
O A:GLY190 3.5 18.0 1.0
C11 A:JG71342 3.7 15.3 1.0
N3 A:JG71342 3.8 12.6 1.0
HA2 A:GLY192 3.8 12.7 1.0
NZ A:LYS187 3.9 32.6 1.0
O A:GLY191 3.9 14.8 1.0
H121 A:JG71342 3.9 16.3 1.0
H112 A:JG71342 4.0 15.7 1.0
O A:HOH2121 4.1 45.8 1.0
HA2 A:GLY191 4.1 13.9 1.0
CA A:GLY192 4.1 12.6 1.0
HZ3 A:LYS187 4.1 32.8 1.0
H92C A:JG71342 4.2 12.2 1.0
N A:GLY191 4.3 14.9 1.0
C A:GLY190 4.3 17.0 1.0
HB2 A:LYS187 4.3 19.7 1.0
O29 A:JG71342 4.4 13.4 1.0
H261 A:JG71342 4.5 13.3 1.0
HG3 A:LYS187 4.5 23.6 1.0
C9 A:JG71342 4.5 12.2 1.0
H111 A:JG71342 4.5 15.5 1.0
CD A:LYS187 4.6 27.7 1.0
O A:GLY192 4.7 11.3 1.0
HZ1 A:LYS187 4.7 30.9 1.0
H91C A:JG71342 4.8 12.7 1.0
C13 A:JG71342 4.8 12.9 1.0
O A:HOH2120 4.8 42.5 1.0
C A:GLY192 4.8 10.9 1.0
HE1 A:TYR193 4.8 13.8 1.0
C7 A:JG71342 4.9 12.1 1.0
HD2 A:LYS187 4.9 27.1 1.0
CG A:LYS187 4.9 24.1 1.0
HA3 A:GLY192 4.9 11.9 1.0

Fluorine binding site 2 out of 6 in 4bs6

Go back to Fluorine Binding Sites List in 4bs6
Fluorine binding site 2 out of 6 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1342

b:17.8
occ:1.00
 F34 A:JG71342 0.0 17.8 1.0
C8 A:JG71342 1.3 17.4 1.0
F33 A:JG71342 2.1 16.0 1.0
F35 A:JG71342 2.2 17.7 1.0
C1 A:JG71342 2.3 15.4 1.0
H112 A:JG71342 2.5 15.7 1.0
H122 A:JG71342 2.5 15.8 1.0
C11 A:JG71342 2.8 15.3 1.0
C12 A:JG71342 2.8 16.2 1.0
HE2 A:LYS187 2.9 30.7 1.0
HZ2 A:LYS187 2.9 32.1 1.0
OH A:TYR193 3.3 18.3 1.0
O A:HOH2132 3.3 25.2 1.0
O A:HOH2120 3.3 42.5 1.0
HE3 A:LYS187 3.3 30.4 1.0
HE1 A:TYR193 3.4 13.8 1.0
CE A:LYS187 3.4 31.6 1.0
NZ A:LYS187 3.6 32.6 1.0
CZ A:TYR193 3.6 15.2 1.0
CE2 A:TYR193 3.7 14.7 1.0
C4 A:JG71342 3.7 14.2 1.0
H111 A:JG71342 3.9 15.5 1.0
H121 A:JG71342 3.9 16.3 1.0
O A:HOH2116 4.1 36.4 1.0
HZ1 A:LYS187 4.2 30.9 1.0
H92C A:JG71342 4.2 12.2 1.0
HZ3 A:LYS187 4.2 32.8 1.0
O28 A:JG71342 4.4 15.3 1.0
H91C A:JG71342 4.4 12.7 1.0
HA2 A:GLY192 4.4 12.7 1.0
N3 A:JG71342 4.5 12.6 1.0
O A:HOH2121 4.6 45.8 1.0
C9 A:JG71342 4.6 12.2 1.0
CE1 A:TYR193 4.6 14.2 1.0
CD2 A:TYR193 4.7 13.6 1.0
HG3 A:LYS187 4.7 23.6 1.0
N A:GLY192 4.8 12.6 1.0
H A:GLY192 4.8 12.8 1.0
CD A:LYS187 4.9 27.7 1.0
HA3 A:GLY191 4.9 13.7 1.0
O A:GLY185 4.9 21.3 1.0
O A:HOH2128 5.0 21.0 1.0
HE2 A:TYR193 5.0 13.9 1.0

Fluorine binding site 3 out of 6 in 4bs6

Go back to Fluorine Binding Sites List in 4bs6
Fluorine binding site 3 out of 6 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1342

b:16.0
occ:1.00
 F33 A:JG71342 0.0 16.0 1.0
C8 A:JG71342 1.3 17.4 1.0
F34 A:JG71342 2.1 17.8 1.0
F35 A:JG71342 2.2 17.7 1.0
C1 A:JG71342 2.4 15.4 1.0
H92C A:JG71342 2.4 12.2 1.0
HA2 A:GLY192 2.8 12.7 1.0
C4 A:JG71342 3.0 14.2 1.0
H A:GLY192 3.0 12.8 1.0
N A:GLY192 3.1 12.6 1.0
C9 A:JG71342 3.1 12.2 1.0
N3 A:JG71342 3.2 12.6 1.0
CE2 A:TYR193 3.2 14.7 1.0
CA A:GLY192 3.2 12.6 1.0
C11 A:JG71342 3.3 15.3 1.0
O A:GLY192 3.3 11.3 1.0
H112 A:JG71342 3.3 15.7 1.0
HE1 A:TYR193 3.3 13.8 1.0
CZ A:TYR193 3.3 15.2 1.0
C A:GLY192 3.4 10.9 1.0
H91C A:JG71342 3.4 12.7 1.0
CD2 A:TYR193 3.6 13.6 1.0
C12 A:JG71342 3.7 16.2 1.0
OH A:TYR193 3.8 18.3 1.0
C A:GLY191 3.8 12.7 1.0
O28 A:JG71342 3.9 15.3 1.0
CE1 A:TYR193 3.9 14.2 1.0
H111 A:JG71342 4.0 15.5 1.0
HD1 A:TYR193 4.0 13.5 1.0
H122 A:JG71342 4.0 15.8 1.0
HA3 A:GLY191 4.0 13.7 1.0
HE2 A:LYS187 4.1 30.7 1.0
CG A:TYR193 4.1 12.8 1.0
HA3 A:GLY192 4.2 11.9 1.0
CD1 A:TYR193 4.2 12.8 1.0
N A:TYR193 4.2 11.6 1.0
HE3 A:LYS187 4.3 30.4 1.0
HE2 A:TYR193 4.4 13.9 1.0
O29 A:JG71342 4.4 13.4 1.0
O A:GLY191 4.4 14.8 1.0
C7 A:JG71342 4.4 12.1 1.0
C5 A:JG71342 4.5 11.3 1.0
CA A:GLY191 4.5 13.9 1.0
H121 A:JG71342 4.6 16.3 1.0
CE A:LYS187 4.6 31.6 1.0
H A:TYR193 4.7 11.3 1.0
H5 A:JG71342 4.7 11.6 1.0
O A:HOH2132 4.8 25.2 1.0
H102 A:JG71342 4.8 11.8 1.0
C13 A:JG71342 4.8 12.9 1.0
HZ2 A:LYS187 4.8 32.1 1.0
O A:GLY185 4.8 21.3 1.0
HA A:TYR193 4.8 11.3 1.0
HA A:ASN186 4.9 16.6 1.0
C10 A:JG71342 4.9 11.7 1.0
HD2 A:TYR193 4.9 12.7 1.0
HA2 A:GLY191 5.0 13.9 1.0
CA A:TYR193 5.0 11.3 1.0

Fluorine binding site 4 out of 6 in 4bs6

Go back to Fluorine Binding Sites List in 4bs6
Fluorine binding site 4 out of 6 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1341

b:18.3
occ:1.00
 F35 B:JG71341 0.0 18.3 1.0
C8 B:JG71341 1.3 16.9 1.0
F33 B:JG71341 2.1 16.7 1.0
F34 B:JG71341 2.2 18.7 1.0
C1 B:JG71341 2.3 15.6 1.0
HA3 B:GLY191 2.7 13.2 1.0
HE3 B:LYS187 2.7 33.4 1.0
HE2 B:LYS187 2.8 31.4 1.0
C4 B:JG71341 2.9 14.2 1.0
CE B:LYS187 3.2 34.2 1.0
O28 B:JG71341 3.2 15.9 1.0
C12 B:JG71341 3.2 16.6 1.0
H122 B:JG71341 3.2 15.7 1.0
C B:GLY191 3.3 13.2 1.0
N B:GLY192 3.3 12.9 1.0
H B:GLY192 3.4 12.9 1.0
CA B:GLY191 3.4 13.2 1.0
O B:HOH2128 3.4 21.0 1.0
HZ2 B:LYS187 3.4 36.9 1.0
O B:GLY190 3.6 17.9 1.0
C11 B:JG71341 3.7 16.0 1.0
HA2 B:GLY192 3.8 12.4 1.0
NZ B:LYS187 3.8 37.7 1.0
O B:GLY191 3.8 15.7 1.0
N3 B:JG71341 3.8 12.8 1.0
H121 B:JG71341 3.9 16.5 1.0
H112 B:JG71341 4.0 16.2 1.0
HA2 B:GLY191 4.1 13.3 1.0
CA B:GLY192 4.1 12.6 1.0
H92C B:JG71341 4.2 12.3 1.0
HB2 B:LYS187 4.2 19.2 1.0
HG3 B:LYS187 4.2 21.9 1.0
N B:GLY191 4.2 13.8 1.0
C B:GLY190 4.3 14.8 1.0
O29 B:JG71341 4.3 12.3 1.0
HZ3 B:LYS187 4.4 36.9 1.0
HZ1 B:LYS187 4.5 36.5 1.0
CD B:LYS187 4.5 27.5 1.0
C9 B:JG71341 4.5 12.3 1.0
H261 B:JG71341 4.5 11.8 1.0
H111 B:JG71341 4.5 16.1 1.0
CG B:LYS187 4.7 21.9 1.0
O B:GLY192 4.7 12.4 1.0
H91C B:JG71341 4.8 12.7 1.0
C13 B:JG71341 4.8 11.6 1.0
C B:GLY192 4.8 12.3 1.0
HE1 B:TYR193 4.8 16.4 1.0
HD2 B:LYS187 4.8 26.7 1.0
HA3 B:GLY192 4.9 12.8 1.0
O B:HOH2120 4.9 43.9 1.0
C7 B:JG71341 4.9 11.9 1.0
CB B:LYS187 4.9 19.4 1.0
O B:HOH2122 5.0 42.8 1.0
H B:GLY191 5.0 13.7 1.0
CE2 B:TYR193 5.0 17.0 1.0

Fluorine binding site 5 out of 6 in 4bs6

Go back to Fluorine Binding Sites List in 4bs6
Fluorine binding site 5 out of 6 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1341

b:18.7
occ:1.00
 F34 B:JG71341 0.0 18.7 1.0
C8 B:JG71341 1.3 16.9 1.0
F33 B:JG71341 2.1 16.7 1.0
F35 B:JG71341 2.2 18.3 1.0
C1 B:JG71341 2.4 15.6 1.0
H112 B:JG71341 2.5 16.2 1.0
H122 B:JG71341 2.6 15.7 1.0
HE2 B:LYS187 2.6 31.4 1.0
HZ2 B:LYS187 2.8 36.9 1.0
C11 B:JG71341 2.8 16.0 1.0
C12 B:JG71341 2.9 16.6 1.0
O B:HOH2133 3.2 28.5 1.0
CE B:LYS187 3.3 34.2 1.0
OH B:TYR193 3.3 20.8 1.0
HE1 B:TYR193 3.3 16.4 1.0
NZ B:LYS187 3.4 37.7 1.0
HE3 B:LYS187 3.4 33.4 1.0
O B:HOH2122 3.4 42.8 1.0
HZ1 B:LYS187 3.6 36.5 1.0
CZ B:TYR193 3.6 16.9 1.0
CE2 B:TYR193 3.6 17.0 1.0
C4 B:JG71341 3.7 14.2 1.0
H111 B:JG71341 3.9 16.1 1.0
H121 B:JG71341 3.9 16.5 1.0
H92C B:JG71341 4.2 12.3 1.0
O B:HOH2118 4.2 31.1 1.0
HZ3 B:LYS187 4.3 36.9 1.0
HA2 B:GLY192 4.4 12.4 1.0
O28 B:JG71341 4.4 15.9 1.0
H91C B:JG71341 4.4 12.7 1.0
HG3 B:LYS187 4.5 21.9 1.0
N3 B:JG71341 4.5 12.8 1.0
C9 B:JG71341 4.6 12.3 1.0
CE1 B:TYR193 4.6 16.5 1.0
CD2 B:TYR193 4.6 16.1 1.0
CD B:LYS187 4.6 27.5 1.0
O B:GLY185 4.7 21.2 1.0
N B:GLY192 4.8 12.9 1.0
HA3 B:GLY191 4.8 13.2 1.0
H B:GLY192 4.8 12.9 1.0
HD3 B:LYS187 4.9 26.9 1.0
HE2 B:TYR193 5.0 16.2 1.0
O B:HOH2128 5.0 21.0 1.0
CA B:GLY192 5.0 12.6 1.0
HD1 B:TYR193 5.0 16.1 1.0

Fluorine binding site 6 out of 6 in 4bs6

Go back to Fluorine Binding Sites List in 4bs6
Fluorine binding site 6 out of 6 in the Mouse Cathepsin S with Covalent Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Mouse Cathepsin S with Covalent Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F1341

b:16.7
occ:1.00
 F33 B:JG71341 0.0 16.7 1.0
C8 B:JG71341 1.3 16.9 1.0
F34 B:JG71341 2.1 18.7 1.0
F35 B:JG71341 2.1 18.3 1.0
C1 B:JG71341 2.4 15.6 1.0
H92C B:JG71341 2.4 12.3 1.0
HA2 B:GLY192 2.8 12.4 1.0
C4 B:JG71341 3.0 14.2 1.0
H B:GLY192 3.0 12.9 1.0
N B:GLY192 3.1 12.9 1.0
C9 B:JG71341 3.1 12.3 1.0
CA B:GLY192 3.2 12.6 1.0
CE2 B:TYR193 3.2 17.0 1.0
N3 B:JG71341 3.2 12.8 1.0
C11 B:JG71341 3.3 16.0 1.0
O B:GLY192 3.3 12.4 1.0
H112 B:JG71341 3.3 16.2 1.0
HE1 B:TYR193 3.3 16.4 1.0
C B:GLY192 3.3 12.3 1.0
CZ B:TYR193 3.4 16.9 1.0
H91C B:JG71341 3.4 12.7 1.0
CD2 B:TYR193 3.6 16.1 1.0
C12 B:JG71341 3.7 16.6 1.0
C B:GLY191 3.8 13.2 1.0
HE2 B:LYS187 3.8 31.4 1.0
OH B:TYR193 3.8 20.8 1.0
O28 B:JG71341 3.9 15.9 1.0
CE1 B:TYR193 3.9 16.5 1.0
HD1 B:TYR193 3.9 16.1 1.0
H111 B:JG71341 4.0 16.1 1.0
H122 B:JG71341 4.0 15.7 1.0
HA3 B:GLY191 4.0 13.2 1.0
CG B:TYR193 4.1 15.2 1.0
HA3 B:GLY192 4.1 12.8 1.0
N B:TYR193 4.2 12.9 1.0
CD1 B:TYR193 4.2 14.4 1.0
O B:GLY191 4.4 15.7 1.0
HE2 B:TYR193 4.4 16.2 1.0
O29 B:JG71341 4.4 12.3 1.0
C7 B:JG71341 4.4 11.9 1.0
HE3 B:LYS187 4.5 33.4 1.0
CA B:GLY191 4.5 13.2 1.0
C5 B:JG71341 4.5 11.6 1.0
CE B:LYS187 4.6 34.2 1.0
H121 B:JG71341 4.6 16.5 1.0
H B:TYR193 4.6 12.8 1.0
H5 B:JG71341 4.7 12.0 1.0
HZ2 B:LYS187 4.7 36.9 1.0
HA B:ASN186 4.8 16.9 1.0
O B:GLY185 4.8 21.2 1.0
O B:HOH2133 4.8 28.5 1.0
H102 B:JG71341 4.8 11.4 1.0
HA B:TYR193 4.8 13.1 1.0
C13 B:JG71341 4.8 11.6 1.0
C10 B:JG71341 4.9 11.2 1.0
HD2 B:TYR193 4.9 14.4 1.0
HG3 B:LYS187 4.9 21.9 1.0
HA2 B:GLY191 4.9 13.3 1.0
CA B:TYR193 5.0 12.9 1.0

Reference:

W.Haap, D.W.Banner. Cathepsin S Nitrile Inhibitors To Be Published.
Page generated: Sun Dec 13 11:59:47 2020

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