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Fluorine in PDB 5qc7: 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: 5qc7 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) 32.73 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.970, 58.500, 59.540, 66.28, 69.76, 72.62
R / Rfree (%) 15.5 / 20.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc7). 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: 5qc7:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5qc7

Go back to Fluorine Binding Sites List in 5qc7
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:18.3
occ:1.00
 F45 A:BQS901 0.0 18.3 1.0
C33 A:BQS901 1.3 16.6 1.0
F46 A:BQS901 2.1 16.1 1.0
F47 A:BQS901 2.2 16.8 1.0
C21 A:BQS901 2.3 13.2 1.0
N A:HIS164 2.8 11.6 1.0
C A:HIS164 2.9 12.1 1.0
C26 A:BQS901 2.9 15.2 1.0
S19 A:BQS901 2.9 14.2 1.0
N A:GLY165 3.1 11.3 1.0
C A:ASN163 3.1 17.2 1.0
CA A:HIS164 3.2 11.5 1.0
O A:HIS164 3.3 13.9 1.0
C22 A:BQS901 3.5 15.4 1.0
O A:ASN163 3.7 16.6 1.0
CA A:ASN163 3.8 16.8 1.0
CA A:GLY165 3.8 14.3 1.0
N A:ASN163 3.9 15.2 1.0
CA A:GLY137 4.1 11.9 1.0
C1 A:EOH903 4.2 22.4 1.0
C25 A:BQS901 4.3 17.5 1.0
O A:EOH903 4.4 18.6 1.0
CG2 A:VAL162 4.5 15.8 1.0
C23 A:BQS901 4.6 16.0 1.0
C A:VAL162 4.6 21.4 1.0
CB A:HIS164 4.7 15.0 1.0
C17 A:BQS901 4.8 14.5 1.0
CB A:VAL162 4.8 13.8 1.0
OG A:SER25 4.9 11.2 1.0
N A:VAL138 4.9 13.8 1.0
C24 A:BQS901 5.0 12.8 1.0
O A:VAL138 5.0 16.2 1.0

Fluorine binding site 2 out of 6 in 5qc7

Go back to Fluorine Binding Sites List in 5qc7
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:16.1
occ:1.00
 F46 A:BQS901 0.0 16.1 1.0
C33 A:BQS901 1.3 16.6 1.0
F47 A:BQS901 2.1 16.8 1.0
F45 A:BQS901 2.1 18.3 1.0
C21 A:BQS901 2.3 13.2 1.0
C26 A:BQS901 3.0 15.2 1.0
O A:EOH903 3.1 18.6 1.0
S19 A:BQS901 3.2 14.2 1.0
C22 A:BQS901 3.3 15.4 1.0
O A:GLY69 3.5 12.3 1.0
C1 A:EOH903 3.5 22.4 1.0
N A:GLY165 3.7 11.3 1.0
CB A:TRP26 3.8 13.9 1.0
CA A:GLY165 3.9 14.3 1.0
SD A:MET71 4.0 13.4 1.0
CA A:TRP26 4.2 13.0 1.0
C A:HIS164 4.2 12.1 1.0
C25 A:BQS901 4.3 17.5 1.0
N A:TRP26 4.4 11.0 1.0
C15 A:BQS901 4.5 18.6 1.0
C23 A:BQS901 4.5 16.0 1.0
C17 A:BQS901 4.6 14.5 1.0
OG A:SER25 4.6 11.2 1.0
C A:GLY69 4.7 14.4 1.0
N A:HIS164 4.7 11.6 1.0
CA A:HIS164 4.7 11.5 1.0
C2 A:EOH903 4.8 18.2 1.0
O A:HIS164 4.8 13.9 1.0
C A:ASN163 4.9 17.2 1.0
CG A:TRP26 4.9 14.2 1.0
C24 A:BQS901 4.9 12.8 1.0
O A:ASN163 4.9 16.6 1.0
CE A:MET71 5.0 11.8 1.0

Fluorine binding site 3 out of 6 in 5qc7

Go back to Fluorine Binding Sites List in 5qc7
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:16.8
occ:1.00
 F47 A:BQS901 0.0 16.8 1.0
C33 A:BQS901 1.3 16.6 1.0
F46 A:BQS901 2.1 16.1 1.0
F45 A:BQS901 2.2 18.3 1.0
C21 A:BQS901 2.3 13.2 1.0
C22 A:BQS901 2.7 15.4 1.0
CA A:GLY165 3.1 14.3 1.0
SD A:MET71 3.3 13.4 1.0
N A:GLY165 3.3 11.3 1.0
CA A:GLY137 3.4 11.9 1.0
CE A:MET71 3.5 11.8 1.0
C A:HIS164 3.6 12.1 1.0
C26 A:BQS901 3.6 15.2 1.0
O A:HIS164 3.7 13.9 1.0
O A:VAL136 3.8 15.7 1.0
N A:GLY137 4.0 15.5 1.0
C23 A:BQS901 4.0 16.0 1.0
C A:VAL136 4.2 15.0 1.0
S19 A:BQS901 4.4 14.2 1.0
C A:GLY165 4.5 13.4 1.0
N A:HIS164 4.6 11.6 1.0
CA A:HIS164 4.6 11.5 1.0
C25 A:BQS901 4.8 17.5 1.0
C A:GLY137 4.8 10.3 1.0
N A:VAL166 4.8 13.6 1.0
C24 A:BQS901 4.9 12.8 1.0

Fluorine binding site 4 out of 6 in 5qc7

Go back to Fluorine Binding Sites List in 5qc7
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:18.6
occ:1.00
 F45 B:BQS901 0.0 18.6 1.0
C33 B:BQS901 1.3 18.1 1.0
F46 B:BQS901 2.2 11.2 1.0
F47 B:BQS901 2.2 14.2 1.0
C21 B:BQS901 2.3 13.8 1.0
N B:HIS164 2.9 12.7 1.0
S19 B:BQS901 2.9 12.4 1.0
C26 B:BQS901 2.9 13.6 1.0
C B:HIS164 3.0 13.4 1.0
N B:GLY165 3.3 12.3 1.0
C B:ASN163 3.3 15.8 1.0
O B:HIS164 3.3 15.3 1.0
CA B:HIS164 3.4 12.0 1.0
C22 B:BQS901 3.5 14.3 1.0
CA B:ASN163 3.8 15.8 1.0
CA B:GLY165 3.9 12.6 1.0
N B:ASN163 3.9 13.7 1.0
O B:ASN163 3.9 13.1 1.0
CA B:GLY137 4.0 10.4 1.0
CG2 B:VAL162 4.1 13.6 1.0
S B:DMS902 4.2 47.9 1.0
C25 B:BQS901 4.2 16.4 1.0
C B:VAL162 4.5 18.1 1.0
CB B:VAL162 4.5 15.2 1.0
C17 B:BQS901 4.6 17.1 1.0
C23 B:BQS901 4.6 13.8 1.0
O B:DMS902 4.7 22.9 1.0
N B:VAL138 4.8 11.9 1.0
CB B:HIS164 4.8 15.8 1.0
O B:VAL162 4.9 12.3 1.0
C B:GLY137 4.9 10.9 1.0
O B:VAL138 5.0 16.4 1.0
C24 B:BQS901 5.0 15.2 1.0

Fluorine binding site 5 out of 6 in 5qc7

Go back to Fluorine Binding Sites List in 5qc7
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:11.2
occ:1.00
 F46 B:BQS901 0.0 11.2 1.0
C33 B:BQS901 1.3 18.1 1.0
F47 B:BQS901 2.1 14.2 1.0
F45 B:BQS901 2.2 18.6 1.0
C21 B:BQS901 2.3 13.8 1.0
C26 B:BQS901 3.1 13.6 1.0
C22 B:BQS901 3.3 14.3 1.0
S19 B:BQS901 3.3 12.4 1.0
O B:DMS902 3.4 22.9 1.0
S B:DMS902 3.6 47.9 1.0
O B:GLY69 3.6 19.8 1.0
N B:GLY165 3.7 12.3 1.0
CA B:GLY165 3.9 12.6 1.0
SD B:MET71 3.9 12.9 1.0
CB B:TRP26 3.9 12.6 1.0
C B:HIS164 4.2 13.4 1.0
CA B:TRP26 4.3 13.4 1.0
C25 B:BQS901 4.3 16.4 1.0
C1 B:DMS902 4.4 25.0 1.0
C15 B:BQS901 4.4 17.6 1.0
C23 B:BQS901 4.5 13.8 1.0
C17 B:BQS901 4.6 17.1 1.0
N B:TRP26 4.6 12.6 1.0
N B:HIS164 4.7 12.7 1.0
CE B:MET71 4.7 9.9 1.0
O B:HIS164 4.7 15.3 1.0
CA B:HIS164 4.8 12.0 1.0
C B:GLY69 4.8 10.6 1.0
OG B:SER25 4.9 11.8 1.0
C24 B:BQS901 4.9 15.2 1.0
C B:ASN163 5.0 15.8 1.0

Fluorine binding site 6 out of 6 in 5qc7

Go back to Fluorine Binding Sites List in 5qc7
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:14.2
occ:1.00
 F47 B:BQS901 0.0 14.2 1.0
C33 B:BQS901 1.3 18.1 1.0
F46 B:BQS901 2.1 11.2 1.0
F45 B:BQS901 2.2 18.6 1.0
C21 B:BQS901 2.4 13.8 1.0
C22 B:BQS901 2.7 14.3 1.0
CA B:GLY165 3.1 12.6 1.0
CA B:GLY137 3.2 10.4 1.0
CE B:MET71 3.4 9.9 1.0
SD B:MET71 3.4 12.9 1.0
N B:GLY165 3.4 12.3 1.0
O B:HIS164 3.6 15.3 1.0
N B:GLY137 3.7 8.9 1.0
C B:HIS164 3.7 13.4 1.0
C26 B:BQS901 3.7 13.6 1.0
O B:VAL136 3.7 12.4 1.0
C B:VAL136 3.9 8.1 1.0
C23 B:BQS901 4.1 13.8 1.0
S19 B:BQS901 4.4 12.4 1.0
C B:GLY165 4.5 15.2 1.0
C B:GLY137 4.6 10.9 1.0
N B:HIS164 4.6 12.7 1.0
CA B:HIS164 4.7 12.0 1.0
CG2 B:VAL162 4.7 13.6 1.0
C25 B:BQS901 4.8 16.4 1.0
N B:VAL166 4.8 10.9 1.0
C24 B:BQS901 4.9 15.2 1.0
N B:VAL138 4.9 11.9 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 06:15:45 2025

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