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Fluorine in PDB 5qc3: 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: 5qc3 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) 32.84 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.311, 36.953, 127.337, 90.00, 93.38, 90.00
R / Rfree (%) 15 / 20.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc3). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc3:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5qc3

Go back to Fluorine Binding Sites List in 5qc3
Fluorine binding site 1 out of 8 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:25.7
occ:1.00
 F13 A:B9Y901 0.0 25.7 1.0
C2 A:B9Y901 1.4 21.2 1.0
C3 A:B9Y901 2.4 15.8 1.0
C1 A:B9Y901 2.4 22.2 1.0
C4 A:B9Y901 2.9 15.1 1.0
C6 A:B9Y901 3.0 11.8 1.0
CG A:LYS64 3.4 20.2 1.0
O A:GLY68 3.4 12.4 1.0
C A:GLY68 3.5 14.3 1.0
N5 A:B9Y901 3.5 15.8 1.0
O A:ASN67 3.6 23.9 1.0
O A:HOH1167 3.8 32.9 1.0
CB A:LYS64 3.8 16.6 1.0
CD A:LYS64 3.8 28.4 1.0
CA A:GLY68 3.8 15.6 1.0
CE A:LYS64 4.0 32.7 1.0
N A:GLY69 4.0 11.1 1.0
N A:LYS64 4.2 13.3 1.0
C A:ASN67 4.3 20.8 1.0
O A:GLY62 4.4 15.4 1.0
N A:GLY68 4.4 15.0 1.0
CA A:GLY69 4.5 11.8 1.0
O A:HOH1182 4.6 30.8 1.0
CA A:LYS64 4.6 19.5 1.0
C15 A:B9Y901 4.7 13.6 1.0
C A:ASN63 4.8 17.5 1.0
O A:HOH1336 4.8 31.9 1.0
CA A:ASN63 4.8 12.8 1.0
NZ A:LYS64 4.9 36.8 1.0

Fluorine binding site 2 out of 8 in 5qc3

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Fluorine binding site 2 out of 8 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:9.4
occ:1.00
 F36 A:B9Y901 0.0 9.4 1.0
C34 A:B9Y901 1.3 12.3 1.0
F40 A:B9Y901 2.1 12.1 1.0
F38 A:B9Y901 2.1 13.8 1.0
C27 A:B9Y901 2.3 9.1 1.0
C26 A:B9Y901 2.7 10.3 1.0
CA A:GLY165 3.2 8.7 1.0
SD A:MET71 3.2 9.3 1.0
CE A:MET71 3.3 8.2 1.0
CA A:GLY137 3.4 7.2 1.0
N A:GLY165 3.5 9.3 1.0
C21 A:B9Y901 3.6 13.0 1.0
O A:VAL136 3.7 9.5 1.0
N A:GLY137 3.8 9.2 1.0
C A:HIS164 3.8 9.8 1.0
O A:HIS164 3.9 9.4 1.0
C A:VAL136 4.1 9.2 1.0
C25 A:B9Y901 4.1 9.4 1.0
S19 A:B9Y901 4.3 13.7 1.0
C A:GLY165 4.6 9.5 1.0
C23 A:B9Y901 4.7 9.6 1.0
N A:HIS164 4.8 9.3 1.0
C A:GLY137 4.8 11.4 1.0
CA A:HIS164 4.8 10.8 1.0
N A:VAL166 4.9 6.3 1.0
C24 A:B9Y901 4.9 10.6 1.0
CG A:MET71 4.9 11.9 1.0

Fluorine binding site 3 out of 8 in 5qc3

Go back to Fluorine Binding Sites List in 5qc3
Fluorine binding site 3 out of 8 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:13.8
occ:1.00
 F38 A:B9Y901 0.0 13.8 1.0
C34 A:B9Y901 1.3 12.3 1.0
F40 A:B9Y901 2.1 12.1 1.0
F36 A:B9Y901 2.1 9.4 1.0
C27 A:B9Y901 2.4 9.1 1.0
C21 A:B9Y901 3.1 13.0 1.0
S19 A:B9Y901 3.2 13.7 1.0
O A:GLY69 3.3 10.9 1.0
C26 A:B9Y901 3.4 10.3 1.0
O A:HOH1178 3.5 14.7 1.0
CB A:TRP26 3.6 9.1 1.0
N A:GLY165 3.8 9.3 1.0
SD A:MET71 3.8 9.3 1.0
CA A:GLY165 3.9 8.7 1.0
CA A:TRP26 4.1 9.4 1.0
C A:HIS164 4.3 9.8 1.0
C23 A:B9Y901 4.4 9.6 1.0
N A:TRP26 4.5 10.1 1.0
C15 A:B9Y901 4.5 13.6 1.0
C A:GLY69 4.5 11.8 1.0
C25 A:B9Y901 4.6 9.4 1.0
C17 A:B9Y901 4.6 13.0 1.0
CE A:MET71 4.8 8.2 1.0
CG A:TRP26 4.8 11.3 1.0
N A:HIS164 4.8 9.3 1.0
CA A:HIS164 4.9 10.8 1.0
OG A:SER25 4.9 10.4 1.0
O A:HIS164 4.9 9.4 1.0
C24 A:B9Y901 5.0 10.6 1.0

Fluorine binding site 4 out of 8 in 5qc3

Go back to Fluorine Binding Sites List in 5qc3
Fluorine binding site 4 out of 8 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
A:F901

b:12.1
occ:1.00
 F40 A:B9Y901 0.0 12.1 1.0
C34 A:B9Y901 1.3 12.3 1.0
F36 A:B9Y901 2.1 9.4 1.0
F38 A:B9Y901 2.1 13.8 1.0
C27 A:B9Y901 2.3 9.1 1.0
S19 A:B9Y901 2.8 13.7 1.0
C21 A:B9Y901 2.9 13.0 1.0
C A:HIS164 3.0 9.8 1.0
N A:HIS164 3.0 9.3 1.0
N A:GLY165 3.1 9.3 1.0
O A:HIS164 3.3 9.4 1.0
CA A:HIS164 3.4 10.8 1.0
C26 A:B9Y901 3.5 10.3 1.0
C A:ASN163 3.5 12.4 1.0
CA A:GLY165 3.6 8.7 1.0
CA A:GLY137 4.0 7.2 1.0
CA A:ASN163 4.1 12.0 1.0
O A:ASN163 4.1 8.5 1.0
N A:ASN163 4.2 12.5 1.0
C23 A:B9Y901 4.2 9.6 1.0
O A:HOH1178 4.5 14.7 1.0
CG2 A:VAL162 4.6 10.9 1.0
C25 A:B9Y901 4.6 9.4 1.0
C17 A:B9Y901 4.6 13.0 1.0
C A:VAL162 4.7 12.5 1.0
CB A:VAL162 4.8 12.2 1.0
CB A:HIS164 4.8 9.6 1.0
N A:VAL138 4.9 8.6 1.0
C24 A:B9Y901 4.9 10.6 1.0
C A:GLY137 5.0 11.4 1.0
N A:GLY137 5.0 9.2 1.0
OG A:SER25 5.0 10.4 1.0

Fluorine binding site 5 out of 8 in 5qc3

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Fluorine binding site 5 out of 8 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:27.0
occ:1.00
 F13 B:B9Y901 0.0 27.0 1.0
C2 B:B9Y901 1.4 19.4 1.0
C1 B:B9Y901 2.4 22.5 1.0
C3 B:B9Y901 2.4 16.3 1.0
C4 B:B9Y901 3.0 14.0 1.0
CG B:LYS64 3.2 22.0 1.0
N5 B:B9Y901 3.3 19.0 1.0
C6 B:B9Y901 3.4 20.5 1.0
CD B:LYS64 3.4 31.4 1.0
O B:GLY68 3.5 15.5 1.0
CB B:LYS64 3.5 20.6 1.0
C B:GLY68 3.7 16.3 1.0
CE B:LYS64 3.7 40.4 1.0
O B:ASN67 3.7 19.2 1.0
CA B:GLY68 4.0 12.7 1.0
N B:LYS64 4.2 13.5 1.0
N B:GLY69 4.3 13.9 1.0
C B:ASN67 4.3 20.3 1.0
N B:GLY68 4.4 17.7 1.0
CA B:LYS64 4.5 15.3 1.0
O B:GLY62 4.5 11.9 1.0
CA B:GLY69 4.8 11.1 1.0
C15 B:B9Y901 4.8 15.8 1.0
NZ B:LYS64 4.8 46.7 1.0
C B:ASN63 4.8 15.4 1.0

Fluorine binding site 6 out of 8 in 5qc3

Go back to Fluorine Binding Sites List in 5qc3
Fluorine binding site 6 out of 8 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:12.5
occ:1.00
 F36 B:B9Y901 0.0 12.5 1.0
C34 B:B9Y901 1.3 13.8 1.0
F40 B:B9Y901 2.0 13.3 1.0
F38 B:B9Y901 2.1 11.0 1.0
C27 B:B9Y901 2.3 13.2 1.0
C26 B:B9Y901 2.7 14.0 1.0
SD B:MET71 3.1 8.9 1.0
CA B:GLY165 3.2 12.0 1.0
CE B:MET71 3.2 11.0 1.0
CA B:GLY137 3.4 10.7 1.0
N B:GLY165 3.5 13.2 1.0
C21 B:B9Y901 3.6 13.5 1.0
C B:HIS164 3.8 12.3 1.0
O B:VAL136 3.9 8.0 1.0
N B:GLY137 3.9 10.1 1.0
O B:HIS164 3.9 12.9 1.0
C25 B:B9Y901 4.1 12.6 1.0
C B:VAL136 4.2 10.9 1.0
S19 B:B9Y901 4.4 14.8 1.0
C B:GLY165 4.6 10.4 1.0
N B:HIS164 4.7 14.4 1.0
C23 B:B9Y901 4.7 13.0 1.0
CA B:HIS164 4.8 12.4 1.0
C B:GLY137 4.8 11.9 1.0
CG B:MET71 4.9 6.9 1.0
CB B:TRP26 4.9 11.7 1.0
CA B:TRP26 4.9 10.5 1.0
C24 B:B9Y901 4.9 12.0 1.0
N B:VAL166 5.0 8.1 1.0
CG2 B:VAL162 5.0 10.0 1.0

Fluorine binding site 7 out of 8 in 5qc3

Go back to Fluorine Binding Sites List in 5qc3
Fluorine binding site 7 out of 8 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
B:F901

b:11.0
occ:1.00
 F38 B:B9Y901 0.0 11.0 1.0
C34 B:B9Y901 1.3 13.8 1.0
F36 B:B9Y901 2.1 12.5 1.0
F40 B:B9Y901 2.2 13.3 1.0
C27 B:B9Y901 2.4 13.2 1.0
C21 B:B9Y901 3.1 13.5 1.0
O B:HOH1154 3.2 17.8 1.0
S19 B:B9Y901 3.2 14.8 1.0
O B:GLY69 3.3 12.7 1.0
C26 B:B9Y901 3.4 14.0 1.0
CB B:TRP26 3.5 11.7 1.0
SD B:MET71 3.8 8.9 1.0
N B:GLY165 3.8 13.2 1.0
CA B:GLY165 4.0 12.0 1.0
CA B:TRP26 4.0 10.5 1.0
N B:TRP26 4.3 11.1 1.0
C23 B:B9Y901 4.4 13.0 1.0
C B:HIS164 4.4 12.3 1.0
C B:GLY69 4.4 12.8 1.0
C15 B:B9Y901 4.6 15.8 1.0
OG B:SER25 4.6 9.8 1.0
C17 B:B9Y901 4.6 12.8 1.0
C25 B:B9Y901 4.6 12.6 1.0
CG B:TRP26 4.6 11.7 1.0
CE B:MET71 4.7 11.0 1.0
N B:HIS164 4.8 14.4 1.0
O B:HOH1182 4.8 24.1 1.0
CA B:HIS164 4.9 12.4 1.0
O B:HIS164 5.0 12.9 1.0
CD1 B:TRP26 5.0 11.4 1.0

Fluorine binding site 8 out of 8 in 5qc3

Go back to Fluorine Binding Sites List in 5qc3
Fluorine binding site 8 out of 8 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
B:F901

b:13.3
occ:1.00
 F40 B:B9Y901 0.0 13.3 1.0
C34 B:B9Y901 1.3 13.8 1.0
F36 B:B9Y901 2.0 12.5 1.0
F38 B:B9Y901 2.2 11.0 1.0
C27 B:B9Y901 2.3 13.2 1.0
N B:HIS164 2.9 14.4 1.0
C21 B:B9Y901 2.9 13.5 1.0
S19 B:B9Y901 3.0 14.8 1.0
C B:HIS164 3.0 12.3 1.0
N B:GLY165 3.1 13.2 1.0
CA B:HIS164 3.3 12.4 1.0
O B:HIS164 3.4 12.9 1.0
C B:ASN163 3.4 16.6 1.0
C26 B:B9Y901 3.5 14.0 1.0
CA B:GLY165 3.7 12.0 1.0
CA B:GLY137 3.9 10.7 1.0
O B:ASN163 4.0 16.3 1.0
CA B:ASN163 4.0 14.6 1.0
N B:ASN163 4.1 14.2 1.0
C23 B:B9Y901 4.2 13.0 1.0
CG2 B:VAL162 4.4 10.0 1.0
O B:HOH1154 4.4 17.8 1.0
C B:VAL162 4.6 12.4 1.0
C25 B:B9Y901 4.6 12.6 1.0
CB B:VAL162 4.7 14.6 1.0
C17 B:B9Y901 4.7 12.8 1.0
OG B:SER25 4.8 9.8 1.0
N B:VAL138 4.8 10.4 1.0
CB B:HIS164 4.8 12.5 1.0
C B:GLY137 4.9 11.9 1.0
O B:HOH1182 4.9 24.1 1.0
O B:VAL162 4.9 12.5 1.0
C24 B:B9Y901 4.9 12.0 1.0
N B:GLY137 5.0 10.1 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 06:13:32 2025

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