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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

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