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Fluorine in PDB 5qc0: Crystal Structure of Human Cathepsin-S with Bound Ligand

Enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand

All present enzymatic activity of Crystal Structure of Human Cathepsin-S with Bound Ligand:
3.4.22.27;

Protein crystallography data

The structure of Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc0 was solved by S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burley, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.67 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.980, 52.930, 58.460, 70.92, 72.06, 73.46
R / Rfree (%) 21.3 / 25.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc0). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc0:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5qc0

Go back to Fluorine Binding Sites List in 5qc0
Fluorine binding site 1 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:24.8
occ:1.00
 F44 A:BQJ901 0.0 24.8 1.0
C33 A:BQJ901 1.4 24.1 1.0
F46 A:BQJ901 2.1 22.0 1.0
F45 A:BQJ901 2.2 23.5 1.0
C21 A:BQJ901 2.4 23.9 1.0
N A:HIS164 2.9 24.5 1.0
C A:HIS164 3.0 23.6 1.0
S19 A:BQJ901 3.0 22.9 1.0
C26 A:BQJ901 3.0 24.9 1.0
N A:GLY165 3.0 22.4 1.0
CA A:HIS164 3.3 24.8 1.0
O A:HIS164 3.4 23.4 1.0
C A:ASN163 3.4 28.3 1.0
C22 A:BQJ901 3.5 25.7 1.0
CA A:GLY165 3.6 22.3 1.0
CA A:GLY137 3.9 22.4 1.0
O A:ASN163 4.0 27.6 1.0
CA A:ASN163 4.0 29.2 1.0
N A:ASN163 4.1 29.1 1.0
O A:HOH1123 4.2 26.5 1.0
C25 A:BQJ901 4.3 24.9 1.0
CG2 A:VAL162 4.4 30.1 1.0
C A:VAL162 4.6 30.9 1.0
CB A:VAL162 4.6 30.4 1.0
C23 A:BQJ901 4.7 25.8 1.0
N A:VAL138 4.7 21.0 1.0
C17 A:BQJ901 4.8 25.4 1.0
CB A:HIS164 4.8 24.9 1.0
OG A:SER25 4.8 26.2 1.0
C A:GLY137 4.9 21.3 1.0
O A:VAL138 4.9 21.8 1.0
C24 A:BQJ901 5.0 26.8 1.0
N A:GLY137 5.0 22.1 1.0

Fluorine binding site 2 out of 6 in 5qc0

Go back to Fluorine Binding Sites List in 5qc0
Fluorine binding site 2 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:23.5
occ:1.00
 F45 A:BQJ901 0.0 23.5 1.0
C33 A:BQJ901 1.4 24.1 1.0
F46 A:BQJ901 2.1 22.0 1.0
F44 A:BQJ901 2.2 24.8 1.0
C21 A:BQJ901 2.4 23.9 1.0
O A:HOH1123 2.8 26.5 1.0
C26 A:BQJ901 3.0 24.9 1.0
S19 A:BQJ901 3.1 22.9 1.0
C22 A:BQJ901 3.4 25.7 1.0
O A:GLY69 3.5 25.7 1.0
CB A:TRP26 3.7 22.6 1.0
N A:GLY165 3.7 22.4 1.0
CA A:GLY165 3.9 22.3 1.0
SD A:MET71 3.9 23.5 1.0
CA A:TRP26 4.1 22.5 1.0
N A:TRP26 4.3 23.5 1.0
C A:HIS164 4.3 23.6 1.0
C25 A:BQJ901 4.3 24.9 1.0
OG A:SER25 4.5 26.2 1.0
C15 A:BQJ901 4.5 27.7 1.0
C17 A:BQJ901 4.6 25.4 1.0
C23 A:BQJ901 4.6 25.8 1.0
N A:HIS164 4.7 24.5 1.0
C A:GLY69 4.7 25.5 1.0
CA A:HIS164 4.7 24.8 1.0
CG A:TRP26 4.8 23.4 1.0
CE A:MET71 4.9 24.7 1.0
C A:ASN163 5.0 28.3 1.0
O A:HIS164 5.0 23.4 1.0

Fluorine binding site 3 out of 6 in 5qc0

Go back to Fluorine Binding Sites List in 5qc0
Fluorine binding site 3 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F901

b:22.0
occ:1.00
 F46 A:BQJ901 0.0 22.0 1.0
C33 A:BQJ901 1.3 24.1 1.0
F44 A:BQJ901 2.1 24.8 1.0
F45 A:BQJ901 2.1 23.5 1.0
C21 A:BQJ901 2.3 23.9 1.0
C22 A:BQJ901 2.7 25.7 1.0
CA A:GLY165 3.0 22.3 1.0
SD A:MET71 3.1 23.5 1.0
N A:GLY165 3.4 22.4 1.0
CE A:MET71 3.4 24.7 1.0
CA A:GLY137 3.5 22.4 1.0
C26 A:BQJ901 3.6 24.9 1.0
C A:HIS164 3.8 23.6 1.0
O A:VAL136 3.8 23.0 1.0
N A:GLY137 4.0 22.1 1.0
O A:HIS164 4.0 23.4 1.0
C23 A:BQJ901 4.1 25.8 1.0
C A:VAL136 4.2 22.9 1.0
S19 A:BQJ901 4.3 22.9 1.0
C A:GLY165 4.5 22.3 1.0
C25 A:BQJ901 4.7 24.9 1.0
N A:HIS164 4.8 24.5 1.0
CA A:HIS164 4.8 24.8 1.0
CG A:MET71 4.8 24.9 1.0
O A:HOH1123 4.9 26.5 1.0
N A:VAL166 4.9 22.1 1.0
CA A:TRP26 4.9 22.5 1.0
C A:GLY137 4.9 21.3 1.0
CB A:TRP26 4.9 22.6 1.0
C24 A:BQJ901 4.9 26.8 1.0

Fluorine binding site 4 out of 6 in 5qc0

Go back to Fluorine Binding Sites List in 5qc0
Fluorine binding site 4 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:29.8
occ:1.00
 F44 B:BQJ901 0.0 29.8 1.0
C33 B:BQJ901 1.3 27.2 1.0
F45 B:BQJ901 2.1 26.1 1.0
F46 B:BQJ901 2.2 24.9 1.0
C21 B:BQJ901 2.4 27.0 1.0
N B:HIS164 2.9 24.1 1.0
S19 B:BQJ901 3.0 27.6 1.0
C26 B:BQJ901 3.0 28.0 1.0
C B:HIS164 3.1 24.0 1.0
N B:GLY165 3.2 24.9 1.0
C B:ASN163 3.4 25.7 1.0
CA B:HIS164 3.5 23.0 1.0
C22 B:BQJ901 3.5 27.9 1.0
O B:HIS164 3.5 23.3 1.0
CA B:GLY165 3.8 25.0 1.0
CA B:GLY137 3.9 22.3 1.0
CA B:ASN163 3.9 26.6 1.0
N B:ASN163 3.9 26.1 1.0
O B:ASN163 4.0 25.7 1.0
CG2 B:VAL162 4.2 26.7 1.0
C25 B:BQJ901 4.3 28.4 1.0
O B:HOH1133 4.4 32.1 1.0
CB B:VAL162 4.4 27.2 1.0
C B:VAL162 4.4 27.1 1.0
C23 B:BQJ901 4.7 28.8 1.0
C17 B:BQJ901 4.7 28.0 1.0
N B:VAL138 4.7 22.2 1.0
O B:VAL162 4.8 25.7 1.0
C B:GLY137 4.8 22.8 1.0
O B:VAL138 4.9 24.7 1.0
CB B:HIS164 4.9 22.5 1.0
N B:GLY137 5.0 23.7 1.0

Fluorine binding site 5 out of 6 in 5qc0

Go back to Fluorine Binding Sites List in 5qc0
Fluorine binding site 5 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:26.1
occ:1.00
 F45 B:BQJ901 0.0 26.1 1.0
C33 B:BQJ901 1.4 27.2 1.0
F44 B:BQJ901 2.1 29.8 1.0
F46 B:BQJ901 2.2 24.9 1.0
C21 B:BQJ901 2.4 27.0 1.0
O B:HOH1133 3.1 32.1 1.0
C26 B:BQJ901 3.1 28.0 1.0
S19 B:BQJ901 3.3 27.6 1.0
C22 B:BQJ901 3.4 27.9 1.0
O B:GLY69 3.6 27.9 1.0
N B:GLY165 3.7 24.9 1.0
SD B:MET71 3.9 26.3 1.0
CB B:TRP26 3.9 24.6 1.0
CA B:GLY165 4.0 25.0 1.0
CA B:TRP26 4.3 24.1 1.0
C B:HIS164 4.3 24.0 1.0
C15 B:BQJ901 4.4 27.9 1.0
C25 B:BQJ901 4.4 28.4 1.0
N B:TRP26 4.6 24.6 1.0
C23 B:BQJ901 4.6 28.8 1.0
C17 B:BQJ901 4.6 28.0 1.0
N B:HIS164 4.7 24.1 1.0
OG B:SER25 4.7 25.6 1.0
C B:GLY69 4.8 27.3 1.0
CA B:HIS164 4.8 23.0 1.0
CE B:MET71 4.8 27.3 1.0
C B:ASN163 5.0 25.7 1.0
O B:HIS164 5.0 23.3 1.0
C24 B:BQJ901 5.0 30.0 1.0

Fluorine binding site 6 out of 6 in 5qc0

Go back to Fluorine Binding Sites List in 5qc0
Fluorine binding site 6 out of 6 in the Crystal Structure of Human Cathepsin-S with Bound Ligand


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:24.9
occ:1.00
 F46 B:BQJ901 0.0 24.9 1.0
C33 B:BQJ901 1.4 27.2 1.0
F44 B:BQJ901 2.2 29.8 1.0
F45 B:BQJ901 2.2 26.1 1.0
C21 B:BQJ901 2.4 27.0 1.0
C22 B:BQJ901 2.7 27.9 1.0
SD B:MET71 3.1 26.3 1.0
CA B:GLY165 3.2 25.0 1.0
CA B:GLY137 3.3 22.3 1.0
CE B:MET71 3.3 27.3 1.0
N B:GLY165 3.5 24.9 1.0
O B:VAL136 3.7 21.7 1.0
C26 B:BQJ901 3.7 28.0 1.0
N B:GLY137 3.7 23.7 1.0
C B:HIS164 3.9 24.0 1.0
O B:HIS164 4.0 23.3 1.0
C B:VAL136 4.0 22.4 1.0
C23 B:BQJ901 4.1 28.8 1.0
S19 B:BQJ901 4.5 27.6 1.0
C B:GLY165 4.6 25.7 1.0
C B:GLY137 4.7 22.8 1.0
N B:HIS164 4.8 24.1 1.0
C25 B:BQJ901 4.8 28.4 1.0
CG2 B:VAL162 4.8 26.7 1.0
CA B:HIS164 4.9 23.0 1.0
N B:VAL166 4.9 25.7 1.0
CG B:MET71 4.9 25.9 1.0

Reference:

S.D.Bembenek, M.K.Ameriks, T.Mirzadegan, H.Yang, C.Shao, S.K.Burley. Crystal Structure of Human Cathepsin-S with Bound Ligand To Be Published.
Page generated: Tue Jul 15 06:12:34 2025

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