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Fluorine in PDB 5qcj: 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: 5qcj 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) 49.12 / 2.00
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 65.445, 65.445, 295.325, 90.00, 90.00, 120.00
R / Rfree (%) 18.5 / 22.2

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qcj). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 9 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qcj:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Fluorine binding site 1 out of 9 in 5qcj

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Fluorine binding site 1 out of 9 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:34.8
occ:1.00
 F39 A:BJY901 0.0 34.8 1.0
C38 A:BJY901 1.3 36.4 1.0
F40 A:BJY901 2.0 35.1 1.0
F41 A:BJY901 2.2 35.4 1.0
C35 A:BJY901 2.3 35.6 1.0
C34 A:BJY901 2.8 39.0 1.0
CA A:GLY165 3.1 26.9 1.0
N A:GLY165 3.2 26.3 1.0
C A:HIS164 3.5 27.8 1.0
C36 A:BJY901 3.6 37.0 1.0
SD A:MET71 3.6 30.8 1.0
CE A:MET71 3.6 29.6 1.0
CA A:GLY137 3.6 29.6 1.0
O A:HIS164 3.6 27.3 1.0
O A:VAL136 4.1 28.9 1.0
C33 A:BJY901 4.2 39.7 1.0
N A:GLY137 4.2 28.2 1.0
N A:HIS164 4.4 31.0 1.0
CA A:HIS164 4.4 29.2 1.0
C A:VAL136 4.5 29.6 1.0
C A:GLY165 4.5 28.0 1.0
C37 A:BJY901 4.7 36.0 1.0
C A:GLY137 4.9 29.4 1.0
C32 A:BJY901 5.0 38.2 1.0
N A:VAL166 5.0 28.0 1.0

Fluorine binding site 2 out of 9 in 5qcj

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Fluorine binding site 2 out of 9 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:35.1
occ:1.00
 F40 A:BJY901 0.0 35.1 1.0
C38 A:BJY901 1.3 36.4 1.0
F39 A:BJY901 2.0 34.8 1.0
F41 A:BJY901 2.1 35.4 1.0
C35 A:BJY901 2.3 35.6 1.0
C34 A:BJY901 3.1 39.0 1.0
C36 A:BJY901 3.2 37.0 1.0
O A:GLY69 3.3 33.0 1.0
SD A:MET71 3.6 30.8 1.0
CB A:TRP26 3.8 30.8 1.0
N A:GLY165 4.0 26.3 1.0
CA A:GLY165 4.1 26.9 1.0
CA A:TRP26 4.1 31.4 1.0
O A:HOH1072 4.1 40.2 1.0
O A:HOH1098 4.2 36.0 1.0
C33 A:BJY901 4.3 39.7 1.0
C A:GLY69 4.4 32.7 1.0
CE A:MET71 4.4 29.6 1.0
N A:TRP26 4.4 31.2 1.0
C37 A:BJY901 4.5 36.0 1.0
C A:HIS164 4.6 27.8 1.0
CA A:PHE70 4.7 33.7 1.0
OG A:SER25 4.8 29.4 1.0
C32 A:BJY901 4.9 38.2 1.0
N A:PHE70 4.9 32.2 1.0

Fluorine binding site 3 out of 9 in 5qcj

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Fluorine binding site 3 out of 9 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:35.4
occ:1.00
 F41 A:BJY901 0.0 35.4 1.0
C38 A:BJY901 1.3 36.4 1.0
F40 A:BJY901 2.1 35.1 1.0
F39 A:BJY901 2.2 34.8 1.0
C35 A:BJY901 2.4 35.6 1.0
C36 A:BJY901 2.8 37.0 1.0
N A:HIS164 3.2 31.0 1.0
C A:ASN163 3.3 32.3 1.0
N A:GLY165 3.4 26.3 1.0
C A:HIS164 3.4 27.8 1.0
CA A:HIS164 3.5 29.2 1.0
C34 A:BJY901 3.6 39.0 1.0
O A:ASN163 3.7 34.6 1.0
O A:HIS164 4.0 27.3 1.0
CA A:ASN163 4.0 32.7 1.0
CA A:GLY165 4.1 26.9 1.0
C37 A:BJY901 4.1 36.0 1.0
N A:ASN163 4.4 32.9 1.0
O A:HOH1098 4.4 36.0 1.0
O A:HOH1072 4.4 40.2 1.0
OG A:SER25 4.6 29.4 1.0
O A:GLY69 4.7 33.0 1.0
C33 A:BJY901 4.8 39.7 1.0
C A:VAL162 4.9 36.0 1.0
O A:HOH1162 4.9 46.9 1.0
CA A:GLY137 4.9 29.6 1.0
C32 A:BJY901 5.0 38.2 1.0

Fluorine binding site 4 out of 9 in 5qcj

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Fluorine binding site 4 out of 9 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:F301

b:36.3
occ:1.00
 F39 B:BJY301 0.0 36.3 1.0
C38 B:BJY301 1.3 35.6 1.0
F40 B:BJY301 2.1 36.4 1.0
F41 B:BJY301 2.1 34.5 1.0
C35 B:BJY301 2.3 34.9 1.0
C34 B:BJY301 2.9 35.5 1.0
CA B:GLY165 3.1 28.8 1.0
N B:GLY165 3.2 27.8 1.0
CA B:GLY137 3.3 27.6 1.0
C B:HIS164 3.4 29.3 1.0
O B:HIS164 3.4 26.9 1.0
C36 B:BJY301 3.5 35.4 1.0
CE B:MET71 3.6 31.4 1.0
SD B:MET71 3.6 30.8 1.0
O B:VAL136 3.9 26.2 1.0
N B:GLY137 4.0 26.3 1.0
N B:HIS164 4.2 32.6 1.0
C33 B:BJY301 4.2 36.6 1.0
C B:VAL136 4.3 27.2 1.0
CA B:HIS164 4.3 29.7 1.0
C B:GLY165 4.5 26.6 1.0
C B:GLY137 4.6 28.1 1.0
C37 B:BJY301 4.7 36.8 1.0
N B:VAL138 4.7 30.3 1.0
C B:ASN163 4.8 36.0 1.0
CG2 B:VAL162 4.9 35.4 1.0
N B:VAL166 4.9 26.7 1.0
C32 B:BJY301 4.9 36.6 1.0

Fluorine binding site 5 out of 9 in 5qcj

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Fluorine binding site 5 out of 9 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:F301

b:36.4
occ:1.00
 F40 B:BJY301 0.0 36.4 1.0
C38 B:BJY301 1.3 35.6 1.0
F41 B:BJY301 2.0 34.5 1.0
F39 B:BJY301 2.1 36.3 1.0
C35 B:BJY301 2.3 34.9 1.0
C34 B:BJY301 3.0 35.5 1.0
C36 B:BJY301 3.3 35.4 1.0
O B:GLY69 3.3 32.3 1.0
SD B:MET71 3.3 30.8 1.0
CB B:TRP26 3.7 31.9 1.0
N B:GLY165 3.9 27.8 1.0
CA B:GLY165 4.0 28.8 1.0
CA B:TRP26 4.0 30.3 1.0
CE B:MET71 4.2 31.4 1.0
C33 B:BJY301 4.3 36.6 1.0
C B:GLY69 4.3 32.9 1.0
N B:TRP26 4.4 31.5 1.0
C37 B:BJY301 4.5 36.8 1.0
C B:HIS164 4.5 29.3 1.0
O B:HOH491 4.5 51.0 1.0
CA B:PHE70 4.5 32.4 1.0
N B:MET71 4.8 31.7 1.0
N B:PHE70 4.8 30.0 1.0
OG B:SER25 4.9 31.5 1.0
C32 B:BJY301 4.9 36.6 1.0
CG B:TRP26 5.0 31.9 1.0
CG B:MET71 5.0 29.4 1.0

Fluorine binding site 6 out of 9 in 5qcj

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Fluorine binding site 6 out of 9 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:F301

b:34.5
occ:1.00
 F41 B:BJY301 0.0 34.5 1.0
C38 B:BJY301 1.3 35.6 1.0
F40 B:BJY301 2.0 36.4 1.0
F39 B:BJY301 2.1 36.3 1.0
C35 B:BJY301 2.3 34.9 1.0
C36 B:BJY301 2.8 35.4 1.0
N B:HIS164 3.2 32.6 1.0
N B:GLY165 3.3 27.8 1.0
C B:ASN163 3.3 36.0 1.0
C B:HIS164 3.4 29.3 1.0
CA B:HIS164 3.5 29.7 1.0
C34 B:BJY301 3.6 35.5 1.0
O B:ASN163 3.6 36.5 1.0
O B:HIS164 3.9 26.9 1.0
CA B:GLY165 4.0 28.8 1.0
CA B:ASN163 4.0 38.7 1.0
C37 B:BJY301 4.1 36.8 1.0
N B:ASN163 4.4 38.1 1.0
O B:GLY69 4.5 32.3 1.0
O B:HOH491 4.5 51.0 1.0
OG B:SER25 4.5 31.5 1.0
C33 B:BJY301 4.8 36.6 1.0
CA B:GLY137 4.9 27.6 1.0
C B:VAL162 5.0 39.8 1.0
C32 B:BJY301 5.0 36.6 1.0

Fluorine binding site 7 out of 9 in 5qcj

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Fluorine binding site 7 out of 9 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 7 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:33.7
occ:1.00
 F39 C:BJY301 0.0 33.7 1.0
C38 C:BJY301 1.3 33.9 1.0
F40 C:BJY301 2.1 33.8 1.0
F41 C:BJY301 2.1 33.0 1.0
C35 C:BJY301 2.3 33.2 1.0
C34 C:BJY301 2.8 33.1 1.0
CA C:GLY165 3.2 28.7 1.0
N C:GLY165 3.3 29.9 1.0
CA C:GLY137 3.4 30.3 1.0
CE C:MET71 3.5 29.3 1.0
SD C:MET71 3.5 28.8 1.0
C36 C:BJY301 3.5 30.6 1.0
C C:HIS164 3.5 31.5 1.0
O C:HIS164 3.6 28.2 1.0
O C:VAL136 4.0 24.3 1.0
N C:GLY137 4.0 29.1 1.0
C33 C:BJY301 4.1 34.4 1.0
C C:VAL136 4.3 27.1 1.0
N C:HIS164 4.3 31.3 1.0
CA C:HIS164 4.5 31.8 1.0
C C:GLY165 4.6 28.4 1.0
C37 C:BJY301 4.7 33.0 1.0
C C:GLY137 4.7 29.8 1.0
N C:VAL138 4.9 26.3 1.0
C32 C:BJY301 4.9 34.5 1.0
C C:ASN163 4.9 31.8 1.0

Fluorine binding site 8 out of 9 in 5qcj

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Fluorine binding site 8 out of 9 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 8 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:33.8
occ:1.00
 F40 C:BJY301 0.0 33.8 1.0
C38 C:BJY301 1.3 33.9 1.0
F41 C:BJY301 2.1 33.0 1.0
F39 C:BJY301 2.1 33.7 1.0
C35 C:BJY301 2.3 33.2 1.0
C34 C:BJY301 3.1 33.1 1.0
O C:GLY69 3.3 33.1 1.0
C36 C:BJY301 3.3 30.6 1.0
SD C:MET71 3.4 28.8 1.0
CB C:TRP26 3.7 32.2 1.0
N C:GLY165 4.0 29.9 1.0
CA C:TRP26 4.0 30.6 1.0
CA C:GLY165 4.1 28.7 1.0
O C:HOH496 4.1 37.6 1.0
O C:HOH443 4.2 51.1 1.0
CE C:MET71 4.3 29.3 1.0
C33 C:BJY301 4.3 34.4 1.0
C C:GLY69 4.4 32.0 1.0
N C:TRP26 4.4 29.9 1.0
C37 C:BJY301 4.5 33.0 1.0
C C:HIS164 4.6 31.5 1.0
CA C:PHE70 4.7 34.3 1.0
OG C:SER25 4.9 28.4 1.0
N C:PHE70 4.9 29.0 1.0
C32 C:BJY301 4.9 34.5 1.0
N C:MET71 5.0 29.8 1.0
CG C:TRP26 5.0 32.8 1.0

Fluorine binding site 9 out of 9 in 5qcj

Go back to Fluorine Binding Sites List in 5qcj
Fluorine binding site 9 out of 9 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 9 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F301

b:33.0
occ:1.00
 F41 C:BJY301 0.0 33.0 1.0
C38 C:BJY301 1.3 33.9 1.0
F40 C:BJY301 2.1 33.8 1.0
F39 C:BJY301 2.1 33.7 1.0
C35 C:BJY301 2.3 33.2 1.0
C36 C:BJY301 2.7 30.6 1.0
N C:HIS164 3.2 31.3 1.0
C C:ASN163 3.3 31.8 1.0
N C:GLY165 3.4 29.9 1.0
C C:HIS164 3.4 31.5 1.0
CA C:HIS164 3.6 31.8 1.0
C34 C:BJY301 3.6 33.1 1.0
O C:ASN163 3.6 31.9 1.0
CA C:ASN163 3.9 33.2 1.0
O C:HIS164 4.0 28.2 1.0
CA C:GLY165 4.1 28.7 1.0
C37 C:BJY301 4.1 33.0 1.0
N C:ASN163 4.3 30.5 1.0
O C:HOH496 4.4 37.6 1.0
O C:HOH443 4.5 51.1 1.0
OG C:SER25 4.7 28.4 1.0
O C:GLY69 4.7 33.1 1.0
C33 C:BJY301 4.7 34.4 1.0
CA C:GLY137 4.8 30.3 1.0
C C:VAL162 4.8 32.6 1.0
C32 C:BJY301 4.9 34.5 1.0
O C:VAL162 5.0 31.7 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 06:17:20 2025

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