Atomistry » Fluorine » PDB 5pzm-5qc0 » 5qbu
Atomistry »
  Fluorine »
    PDB 5pzm-5qc0 »
      5qbu »

Fluorine in PDB 5qbu: 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: 5qbu 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) 44.61 / 2.78
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 114.193, 37.114, 105.854, 90.00, 108.83, 90.00
R / Rfree (%) 18.8 / 23.4

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 5qbu

Go back to Fluorine Binding Sites List in 5qbu
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:21.9
occ:1.00
 F91 A:B8J901 0.0 21.9 1.0
C87 A:B8J901 1.3 23.9 1.0
F93 A:B8J901 2.1 23.9 1.0
F97 A:B8J901 2.2 23.4 1.0
C78 A:B8J901 2.4 25.4 1.0
C79 A:B8J901 3.1 26.3 1.0
O A:HOH1018 3.2 6.7 1.0
O A:GLY69 3.3 19.9 1.0
C77 A:B8J901 3.4 25.5 1.0
CB A:TRP26 3.4 14.4 1.0
SD A:MET71 3.5 18.8 1.0
CA A:TRP26 3.8 15.4 1.0
N A:GLY165 4.0 16.4 1.0
CA A:GLY165 4.0 16.6 1.0
N A:TRP26 4.2 16.5 1.0
C80 A:B8J901 4.4 26.9 1.0
C A:GLY69 4.4 18.7 1.0
CA A:PHE70 4.5 17.2 1.0
CE A:MET71 4.5 20.1 1.0
CG A:TRP26 4.6 13.6 1.0
C76 A:B8J901 4.6 25.4 1.0
C A:HIS164 4.6 17.2 1.0
N A:MET71 4.8 17.0 1.0
OG A:SER25 4.8 18.5 1.0
N A:PHE70 4.9 17.7 1.0
CD1 A:TRP26 5.0 13.6 1.0
N A:HIS164 5.0 19.6 1.0
C74 A:B8J901 5.0 26.6 1.0

Fluorine binding site 2 out of 6 in 5qbu

Go back to Fluorine Binding Sites List in 5qbu
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:23.9
occ:1.00
 F93 A:B8J901 0.0 23.9 1.0
C87 A:B8J901 1.3 23.9 1.0
F91 A:B8J901 2.1 21.9 1.0
F97 A:B8J901 2.1 23.4 1.0
C78 A:B8J901 2.3 25.4 1.0
C79 A:B8J901 2.8 26.3 1.0
CA A:GLY165 3.1 16.6 1.0
N A:GLY165 3.2 16.4 1.0
CA A:GLY137 3.4 14.5 1.0
C A:HIS164 3.4 17.2 1.0
C77 A:B8J901 3.5 25.5 1.0
O A:HIS164 3.6 16.9 1.0
SD A:MET71 3.6 18.8 1.0
CE A:MET71 3.9 20.1 1.0
O A:VAL136 4.0 12.7 1.0
N A:HIS164 4.1 19.6 1.0
N A:GLY137 4.1 14.1 1.0
C80 A:B8J901 4.1 26.9 1.0
CA A:HIS164 4.3 18.8 1.0
C A:VAL136 4.4 13.3 1.0
C A:GLY165 4.6 15.9 1.0
C76 A:B8J901 4.6 25.4 1.0
C A:GLY137 4.7 14.8 1.0
O A:HOH1018 4.7 6.7 1.0
CG2 A:VAL162 4.7 24.6 1.0
C A:ASN163 4.8 20.1 1.0
N A:VAL138 4.8 16.4 1.0
C74 A:B8J901 4.9 26.6 1.0
N A:VAL166 5.0 15.5 1.0

Fluorine binding site 3 out of 6 in 5qbu

Go back to Fluorine Binding Sites List in 5qbu
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:23.4
occ:1.00
 F97 A:B8J901 0.0 23.4 1.0
C87 A:B8J901 1.3 23.9 1.0
F93 A:B8J901 2.1 23.9 1.0
F91 A:B8J901 2.2 21.9 1.0
C78 A:B8J901 2.4 25.4 1.0
C77 A:B8J901 2.8 25.5 1.0
N A:HIS164 3.0 19.6 1.0
O A:HOH1018 3.0 6.7 1.0
C A:ASN163 3.2 20.1 1.0
N A:GLY165 3.4 16.4 1.0
C A:HIS164 3.4 17.2 1.0
CA A:HIS164 3.4 18.8 1.0
O A:ASN163 3.5 20.0 1.0
C79 A:B8J901 3.6 26.3 1.0
CA A:ASN163 3.9 21.3 1.0
O A:HIS164 4.0 16.9 1.0
CA A:GLY165 4.1 16.6 1.0
C76 A:B8J901 4.1 25.4 1.0
N A:ASN163 4.3 22.3 1.0
OG A:SER25 4.5 18.5 1.0
O A:GLY69 4.6 19.9 1.0
C80 A:B8J901 4.8 26.9 1.0
CA A:GLY137 4.9 14.5 1.0
CB A:HIS164 4.9 18.7 1.0
C A:VAL162 4.9 23.7 1.0
C74 A:B8J901 5.0 26.6 1.0

Fluorine binding site 4 out of 6 in 5qbu

Go back to Fluorine Binding Sites List in 5qbu
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:19.6
occ:1.00
 F91 B:B8J901 0.0 19.6 1.0
C87 B:B8J901 1.3 20.5 1.0
F97 B:B8J901 2.1 20.1 1.0
F93 B:B8J901 2.2 19.9 1.0
C78 B:B8J901 2.4 21.1 1.0
C79 B:B8J901 3.0 21.1 1.0
SD B:MET71 3.1 21.0 1.0
CB B:TRP26 3.4 21.7 1.0
O B:GLY69 3.4 21.6 1.0
C77 B:B8J901 3.4 21.3 1.0
CA B:TRP26 3.7 21.9 1.0
CA B:GLY165 3.9 16.0 1.0
N B:GLY165 4.0 16.4 1.0
CE B:MET71 4.2 20.8 1.0
N B:TRP26 4.2 21.5 1.0
C80 B:B8J901 4.3 21.4 1.0
CA B:PHE70 4.4 18.5 1.0
C B:GLY69 4.5 20.3 1.0
N B:MET71 4.6 18.6 1.0
CG B:TRP26 4.6 20.9 1.0
C76 B:B8J901 4.6 21.7 1.0
C B:HIS164 4.6 16.8 1.0
CG B:MET71 4.7 20.4 1.0
N B:PHE70 4.9 19.4 1.0
C B:PHE70 4.9 18.3 1.0
OG B:SER25 5.0 24.0 1.0
C74 B:B8J901 5.0 22.3 1.0

Fluorine binding site 5 out of 6 in 5qbu

Go back to Fluorine Binding Sites List in 5qbu
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:19.9
occ:1.00
 F93 B:B8J901 0.0 19.9 1.0
C87 B:B8J901 1.3 20.5 1.0
F97 B:B8J901 2.1 20.1 1.0
F91 B:B8J901 2.2 19.6 1.0
C78 B:B8J901 2.3 21.1 1.0
C79 B:B8J901 2.9 21.1 1.0
CA B:GLY165 3.1 16.0 1.0
N B:GLY165 3.1 16.4 1.0
CA B:GLY137 3.2 16.0 1.0
C B:HIS164 3.3 16.8 1.0
C77 B:B8J901 3.4 21.3 1.0
O B:HIS164 3.4 16.7 1.0
SD B:MET71 3.8 21.0 1.0
N B:HIS164 3.9 17.6 1.0
CE B:MET71 4.0 20.8 1.0
N B:GLY137 4.0 15.2 1.0
O B:VAL136 4.1 14.8 1.0
CA B:HIS164 4.1 17.4 1.0
C80 B:B8J901 4.2 21.4 1.0
C B:VAL136 4.4 14.7 1.0
C B:GLY137 4.5 17.1 1.0
C76 B:B8J901 4.5 21.7 1.0
C B:GLY165 4.6 15.8 1.0
CG2 B:VAL162 4.6 16.7 1.0
N B:VAL138 4.6 18.4 1.0
C B:ASN163 4.7 17.0 1.0
C74 B:B8J901 4.9 22.3 1.0
N B:VAL166 5.0 15.2 1.0

Fluorine binding site 6 out of 6 in 5qbu

Go back to Fluorine Binding Sites List in 5qbu
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:20.1
occ:1.00
 F97 B:B8J901 0.0 20.1 1.0
C87 B:B8J901 1.3 20.5 1.0
F91 B:B8J901 2.1 19.6 1.0
F93 B:B8J901 2.1 19.9 1.0
C78 B:B8J901 2.4 21.1 1.0
C77 B:B8J901 2.7 21.3 1.0
N B:HIS164 3.4 17.6 1.0
N B:GLY165 3.4 16.4 1.0
C B:ASN163 3.6 17.0 1.0
C B:HIS164 3.6 16.8 1.0
C79 B:B8J901 3.7 21.1 1.0
CA B:HIS164 3.7 17.4 1.0
O B:ASN163 3.8 16.7 1.0
CA B:GLY165 4.1 16.0 1.0
C76 B:B8J901 4.1 21.7 1.0
O B:GLY69 4.2 21.6 1.0
CA B:ASN163 4.2 17.1 1.0
O B:HIS164 4.3 16.7 1.0
OG B:SER25 4.4 24.0 1.0
N B:ASN163 4.7 16.8 1.0
C80 B:B8J901 4.8 21.4 1.0
CB B:TRP26 4.8 21.7 1.0
C74 B:B8J901 5.0 22.3 1.0
N B:TRP26 5.0 21.5 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 06:11:56 2025

Last articles

Fe in 2YXO
Fe in 2YRS
Fe in 2YXC
Fe in 2YNM
Fe in 2YVJ
Fe in 2YP1
Fe in 2YU2
Fe in 2YU1
Fe in 2YQB
Fe in 2YOO
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy