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Fluorine in PDB 2fq9: Cathepsin S with Nitrile Inhibitor

Enzymatic activity of Cathepsin S with Nitrile Inhibitor

All present enzymatic activity of Cathepsin S with Nitrile Inhibitor:
3.4.22.27;

Protein crystallography data

The structure of Cathepsin S with Nitrile Inhibitor, PDB code: 2fq9 was solved by J.R.Somoza, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 26.80 / 1.65
Space group P 41 2 2
Cell size a, b, c (Å), α, β, γ (°) 85.239, 85.239, 150.966, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 21.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cathepsin S with Nitrile Inhibitor (pdb code 2fq9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Cathepsin S with Nitrile Inhibitor, PDB code: 2fq9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 2fq9

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Fluorine binding site 1 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:17.6
occ:1.00
 F7 A:CRJ999 0.0 17.6 1.0
C2 A:CRJ999 1.3 14.6 1.0
C3 A:CRJ999 2.4 11.9 1.0
C1 A:CRJ999 2.4 13.4 1.0
CG A:LYS61 3.1 12.8 1.0
CD A:LYS61 3.2 15.3 1.0
O A:GLY59 3.5 9.4 1.0
CE A:LYS61 3.5 18.7 1.0
C4 A:CRJ999 3.6 12.6 1.0
CB A:LYS61 3.7 11.3 1.0
C6 A:CRJ999 3.7 11.5 1.0
N A:LYS61 3.8 9.3 1.0
O A:GLY65 3.9 9.1 1.0
O A:HOH9320 4.0 13.7 1.0
C5 A:CRJ999 4.2 10.4 1.0
C A:ASN60 4.2 9.4 1.0
C A:GLY65 4.2 8.5 1.0
CA A:ASN60 4.3 9.0 1.0
NZ A:LYS61 4.3 20.4 1.0
CA A:LYS61 4.4 9.9 1.0
C A:GLY59 4.5 9.6 1.0
N A:GLY66 4.6 8.8 1.0
O A:ASN64 4.7 12.9 1.0
CA A:GLY66 4.8 7.7 1.0
CA A:GLY65 4.9 8.9 1.0
N A:ASN60 4.9 9.1 1.0
O A:ASN60 4.9 10.4 1.0
OD1 B:ASN156 4.9 19.2 1.0

Fluorine binding site 2 out of 8 in 2fq9

Go back to Fluorine Binding Sites List in 2fq9
Fluorine binding site 2 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:15.1
occ:1.00
 F29 A:CRJ999 0.0 15.1 1.0
C10 A:CRJ999 1.4 13.4 1.0
F30 A:CRJ999 2.2 17.8 1.0
F31 A:CRJ999 2.2 13.5 1.0
C8 A:CRJ999 2.4 11.2 1.0
N9 A:CRJ999 2.9 8.8 1.0
C5 A:CRJ999 3.1 10.4 1.0
N22 A:CRJ999 3.1 15.0 1.0
C4 A:CRJ999 3.2 12.6 1.0
C21 A:CRJ999 3.4 16.8 1.0
C15 A:CRJ999 3.6 12.1 1.0
O23 A:CRJ999 3.6 18.3 1.0
C18 A:CRJ999 3.7 13.4 1.0
C11 A:CRJ999 4.0 9.3 1.0
C19 A:CRJ999 4.0 17.1 1.0
CE2 A:PHE67 4.0 10.6 1.0
C20 A:CRJ999 4.2 16.8 1.0
C6 A:CRJ999 4.3 11.5 1.0
O27 A:CRJ999 4.3 8.6 1.0
O A:HOH9387 4.4 32.6 1.0
C3 A:CRJ999 4.4 11.9 1.0
CD2 A:PHE67 4.5 10.7 1.0
CZ A:PHE67 4.5 10.0 1.0
S14 A:CRJ999 4.5 8.9 1.0
C13 A:CRJ999 4.7 9.4 1.0
O A:GLY66 4.9 6.9 1.0

Fluorine binding site 3 out of 8 in 2fq9

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Fluorine binding site 3 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:17.8
occ:1.00
 F30 A:CRJ999 0.0 17.8 1.0
C10 A:CRJ999 1.4 13.4 1.0
F29 A:CRJ999 2.2 15.1 1.0
F31 A:CRJ999 2.2 13.5 1.0
C8 A:CRJ999 2.4 11.2 1.0
C5 A:CRJ999 2.9 10.4 1.0
C6 A:CRJ999 3.4 11.5 1.0
C4 A:CRJ999 3.7 12.6 1.0
N9 A:CRJ999 3.7 8.8 1.0
O A:HOH9387 3.8 32.6 1.0
O23 A:CRJ999 4.5 18.3 1.0
N22 A:CRJ999 4.5 15.0 1.0
C1 A:CRJ999 4.5 13.4 1.0
C11 A:CRJ999 4.6 9.3 1.0
C3 A:CRJ999 4.7 11.9 1.0
C21 A:CRJ999 4.8 16.8 1.0

Fluorine binding site 4 out of 8 in 2fq9

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Fluorine binding site 4 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F999

b:13.5
occ:1.00
 F31 A:CRJ999 0.0 13.5 1.0
C10 A:CRJ999 1.4 13.4 1.0
F30 A:CRJ999 2.2 17.8 1.0
F29 A:CRJ999 2.2 15.1 1.0
C8 A:CRJ999 2.4 11.2 1.0
N9 A:CRJ999 3.0 8.8 1.0
N22 A:CRJ999 3.0 15.0 1.0
O27 A:CRJ999 3.1 8.6 1.0
C11 A:CRJ999 3.3 9.3 1.0
O A:HOH9387 3.4 32.6 1.0
O A:VAL157 3.5 10.8 1.0
C21 A:CRJ999 3.7 16.8 1.0
CA A:ASN158 3.7 10.0 1.0
C5 A:CRJ999 3.7 10.4 1.0
O23 A:CRJ999 3.8 18.3 1.0
C15 A:CRJ999 3.9 12.1 1.0
S14 A:CRJ999 3.9 8.9 1.0
C18 A:CRJ999 3.9 13.4 1.0
C13 A:CRJ999 4.2 9.4 1.0
O A:ASN158 4.2 9.4 1.0
C A:ASN158 4.3 9.9 1.0
C A:VAL157 4.4 9.8 1.0
CB A:ASN158 4.5 11.8 1.0
C4 A:CRJ999 4.6 12.6 1.0
N A:ASN158 4.6 9.5 1.0
C12 A:CRJ999 4.6 9.3 1.0
C6 A:CRJ999 4.6 11.5 1.0
C19 A:CRJ999 4.9 17.1 1.0
N16 A:CRJ999 5.0 11.0 1.0
C20 A:CRJ999 5.0 16.8 1.0

Fluorine binding site 5 out of 8 in 2fq9

Go back to Fluorine Binding Sites List in 2fq9
Fluorine binding site 5 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F998

b:11.9
occ:1.00
 F7 B:CRJ998 0.0 11.9 1.0
C2 B:CRJ998 1.3 10.3 1.0
C3 B:CRJ998 2.4 11.4 1.0
C1 B:CRJ998 2.4 10.8 1.0
CG B:LYS61 3.1 11.9 1.0
O B:GLY59 3.1 9.7 1.0
CE B:LYS61 3.3 18.5 1.0
CD B:LYS61 3.4 12.8 1.0
O A:HOH9319 3.6 16.0 1.0
C4 B:CRJ998 3.6 10.4 1.0
C6 B:CRJ998 3.7 9.5 1.0
CB B:LYS61 3.8 8.7 1.0
N B:LYS61 3.8 9.0 1.0
O B:GLY65 3.9 8.8 1.0
CA B:ASN60 4.0 7.6 1.0
C B:ASN60 4.0 8.3 1.0
C B:GLY59 4.1 9.4 1.0
C5 B:CRJ998 4.2 9.9 1.0
C B:GLY65 4.3 8.3 1.0
ND2 A:ASN156 4.4 22.0 1.0
NZ B:LYS61 4.4 18.2 1.0
CA B:LYS61 4.5 9.0 1.0
N B:ASN60 4.5 8.1 1.0
N B:GLY66 4.7 8.4 1.0
CA B:GLY66 4.7 7.7 1.0
O B:ASN60 4.8 9.9 1.0
O A:HOH9307 4.9 17.4 1.0
CE1 B:PHE67 4.9 9.9 1.0
O B:ASN64 5.0 9.9 1.0

Fluorine binding site 6 out of 8 in 2fq9

Go back to Fluorine Binding Sites List in 2fq9
Fluorine binding site 6 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F998

b:17.0
occ:1.00
 F29 B:CRJ998 0.0 17.0 1.0
C10 B:CRJ998 1.4 13.9 1.0
F31 B:CRJ998 2.2 17.9 1.0
F30 B:CRJ998 2.2 16.9 1.0
C8 B:CRJ998 2.4 10.3 1.0
N9 B:CRJ998 2.9 8.4 1.0
C5 B:CRJ998 3.0 9.9 1.0
C4 B:CRJ998 3.1 10.4 1.0
N22 B:CRJ998 3.3 14.8 1.0
C21 B:CRJ998 3.5 17.9 1.0
O23 B:CRJ998 3.7 20.1 1.0
CE2 B:PHE67 3.9 12.0 1.0
C15 B:CRJ998 3.9 11.2 1.0
C18 B:CRJ998 4.0 14.9 1.0
C11 B:CRJ998 4.1 9.3 1.0
C6 B:CRJ998 4.3 9.5 1.0
C19 B:CRJ998 4.3 15.8 1.0
C3 B:CRJ998 4.4 11.4 1.0
C20 B:CRJ998 4.4 17.6 1.0
O27 B:CRJ998 4.4 8.8 1.0
CD2 B:PHE67 4.4 10.4 1.0
CZ B:PHE67 4.5 9.8 1.0
S14 B:CRJ998 4.7 8.6 1.0
C13 B:CRJ998 4.8 9.0 1.0
O B:GLY66 4.9 8.2 1.0

Fluorine binding site 7 out of 8 in 2fq9

Go back to Fluorine Binding Sites List in 2fq9
Fluorine binding site 7 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 7 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F998

b:16.9
occ:1.00
 F30 B:CRJ998 0.0 16.9 1.0
C10 B:CRJ998 1.4 13.9 1.0
F31 B:CRJ998 2.2 17.9 1.0
F29 B:CRJ998 2.2 17.0 1.0
C8 B:CRJ998 2.4 10.3 1.0
C5 B:CRJ998 2.9 9.9 1.0
C6 B:CRJ998 3.5 9.5 1.0
N9 B:CRJ998 3.7 8.4 1.0
C4 B:CRJ998 3.7 10.4 1.0
O B:HOH9386 3.9 21.8 1.0
O B:HOH9408 4.6 20.9 1.0
C1 B:CRJ998 4.6 10.8 1.0
C11 B:CRJ998 4.6 9.3 1.0
C3 B:CRJ998 4.7 11.4 1.0
O23 B:CRJ998 4.8 20.1 1.0
N22 B:CRJ998 4.8 14.8 1.0

Fluorine binding site 8 out of 8 in 2fq9

Go back to Fluorine Binding Sites List in 2fq9
Fluorine binding site 8 out of 8 in the Cathepsin S with Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 8 of Cathepsin S with Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F998

b:17.9
occ:1.00
 F31 B:CRJ998 0.0 17.9 1.0
C10 B:CRJ998 1.4 13.9 1.0
F30 B:CRJ998 2.2 16.9 1.0
F29 B:CRJ998 2.2 17.0 1.0
C8 B:CRJ998 2.4 10.3 1.0
N9 B:CRJ998 2.9 8.4 1.0
O27 B:CRJ998 3.2 8.8 1.0
N22 B:CRJ998 3.2 14.8 1.0
C11 B:CRJ998 3.3 9.3 1.0
O B:HOH9386 3.4 21.8 1.0
C5 B:CRJ998 3.8 9.9 1.0
O B:VAL157 3.8 11.5 1.0
C21 B:CRJ998 3.9 17.9 1.0
O23 B:CRJ998 4.0 20.1 1.0
S14 B:CRJ998 4.0 8.6 1.0
C15 B:CRJ998 4.0 11.2 1.0
CA B:ASN158 4.1 10.3 1.0
C18 B:CRJ998 4.2 14.9 1.0
C13 B:CRJ998 4.2 9.0 1.0
O B:ASN158 4.3 8.7 1.0
C12 B:CRJ998 4.5 9.3 1.0
C B:ASN158 4.5 9.1 1.0
C4 B:CRJ998 4.5 10.4 1.0
C B:VAL157 4.6 11.0 1.0
C6 B:CRJ998 4.7 9.5 1.0
N B:ASN158 4.8 9.9 1.0
N16 B:CRJ998 4.8 9.2 1.0
CB B:ASN158 4.9 10.8 1.0

Reference:

J.R.Somoza, J.R.Somoza. N/A N/A.
Page generated: Wed Jul 31 14:23:43 2024

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