Atomistry » Fluorine » PDB 5pzl-5qbz » 5qbu
Atomistry »
  Fluorine »
    PDB 5pzl-5qbz »
      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: Thu Aug 1 12:58:49 2024

Last articles

Zn in 9JPJ
Zn in 9JP7
Zn in 9JPK
Zn in 9JPL
Zn in 9GN6
Zn in 9GN7
Zn in 9GKU
Zn in 9GKW
Zn in 9GKX
Zn in 9GL0
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy