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Fluorine in PDB 5qc9: 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: 5qc9 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) 32.47 / 2.00
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.088, 57.914, 59.044, 102.44, 107.47, 106.22
R / Rfree (%) 13.6 / 16.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc9). 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: 5qc9:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5qc9

Go back to Fluorine Binding Sites List in 5qc9
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:13.8
occ:1.00
 F56 A:BG7901 0.0 13.8 1.0
C54 A:BG7901 1.3 13.0 1.0
F60 A:BG7901 2.1 14.4 1.0
F58 A:BG7901 2.1 19.5 1.0
C45 A:BG7901 2.3 11.9 1.0
C44 A:BG7901 3.0 12.8 1.0
C62 A:BG7901 3.0 11.8 1.0
O A:GLY69 3.2 13.5 1.0
O A:HOH1219 3.3 24.5 1.0
C46 A:BG7901 3.4 11.4 1.0
N64 A:BG7901 3.5 13.9 1.0
CB A:TRP26 3.8 11.1 1.0
N A:GLY165 3.9 11.2 1.0
SD A:MET71 3.9 11.4 1.0
O A:HOH1216 4.1 22.7 1.0
CA A:GLY165 4.1 10.6 1.0
C43 A:BG7901 4.3 12.3 1.0
CA A:TRP26 4.3 12.1 1.0
C A:GLY69 4.4 11.2 1.0
C A:HIS164 4.4 11.0 1.0
C47 A:BG7901 4.6 12.4 1.0
N A:TRP26 4.7 11.9 1.0
CE A:MET71 4.7 10.3 1.0
C66 A:BG7901 4.8 19.6 1.0
N A:HIS164 4.8 11.0 1.0
CA A:PHE70 4.9 10.6 1.0
CA A:HIS164 4.9 10.2 1.0
CG A:TRP26 5.0 12.8 1.0
O A:HIS164 5.0 11.4 1.0
C41 A:BG7901 5.0 13.7 1.0

Fluorine binding site 2 out of 6 in 5qc9

Go back to Fluorine Binding Sites List in 5qc9
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:19.5
occ:1.00
 F58 A:BG7901 0.0 19.5 1.0
C54 A:BG7901 1.3 13.0 1.0
F60 A:BG7901 2.1 14.4 1.0
F56 A:BG7901 2.1 13.8 1.0
C45 A:BG7901 2.4 11.9 1.0
C44 A:BG7901 3.0 12.8 1.0
C62 A:BG7901 3.1 11.8 1.0
N A:HIS164 3.1 11.0 1.0
C A:HIS164 3.2 11.0 1.0
C46 A:BG7901 3.4 11.4 1.0
N A:GLY165 3.4 11.2 1.0
C A:ASN163 3.4 14.8 1.0
O A:HIS164 3.5 11.4 1.0
CA A:HIS164 3.6 10.2 1.0
CA A:ASN163 3.9 13.8 1.0
CA A:GLY165 3.9 10.6 1.0
N A:ASN163 4.0 10.4 1.0
O A:ASN163 4.0 11.7 1.0
CA A:GLY137 4.0 10.1 1.0
CG2 A:VAL162 4.2 12.6 1.0
O A:HOH1219 4.2 24.5 1.0
N64 A:BG7901 4.2 13.9 1.0
C43 A:BG7901 4.3 12.3 1.0
C A:VAL162 4.4 15.3 1.0
CB A:VAL162 4.5 13.7 1.0
C47 A:BG7901 4.6 12.4 1.0
O A:VAL162 4.8 10.2 1.0
O A:HOH1216 5.0 22.7 1.0
C41 A:BG7901 5.0 13.7 1.0
N A:VAL138 5.0 10.5 1.0

Fluorine binding site 3 out of 6 in 5qc9

Go back to Fluorine Binding Sites List in 5qc9
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:14.4
occ:1.00
 F60 A:BG7901 0.0 14.4 1.0
C54 A:BG7901 1.3 13.0 1.0
F56 A:BG7901 2.1 13.8 1.0
F58 A:BG7901 2.1 19.5 1.0
C45 A:BG7901 2.4 11.9 1.0
C46 A:BG7901 2.7 11.4 1.0
SD A:MET71 3.2 11.4 1.0
CA A:GLY165 3.2 10.6 1.0
CE A:MET71 3.2 10.3 1.0
CA A:GLY137 3.5 10.1 1.0
N A:GLY165 3.5 11.2 1.0
C44 A:BG7901 3.7 12.8 1.0
C A:HIS164 3.8 11.0 1.0
O A:HIS164 3.9 11.4 1.0
O A:VAL136 3.9 9.8 1.0
N A:GLY137 4.0 10.7 1.0
C47 A:BG7901 4.1 12.4 1.0
C A:VAL136 4.2 10.5 1.0
C62 A:BG7901 4.3 11.8 1.0
C A:GLY165 4.6 10.1 1.0
N A:HIS164 4.8 11.0 1.0
C43 A:BG7901 4.8 12.3 1.0
CA A:HIS164 4.8 10.2 1.0
C A:GLY137 4.9 11.1 1.0
C41 A:BG7901 4.9 13.7 1.0
CG2 A:VAL162 4.9 12.6 1.0
CG A:MET71 5.0 9.0 1.0

Fluorine binding site 4 out of 6 in 5qc9

Go back to Fluorine Binding Sites List in 5qc9
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:14.1
occ:1.00
 F56 B:BG7901 0.0 14.1 1.0
C54 B:BG7901 1.3 14.4 1.0
F60 B:BG7901 2.1 15.2 1.0
F58 B:BG7901 2.1 16.8 1.0
C45 B:BG7901 2.3 14.6 1.0
C44 B:BG7901 3.0 16.2 1.0
C62 B:BG7901 3.0 14.1 1.0
O B:HOH1202 3.3 21.9 1.0
O B:GLY69 3.3 12.7 1.0
C46 B:BG7901 3.4 14.3 1.0
N64 B:BG7901 3.5 16.6 1.0
CB B:TRP26 3.7 10.1 1.0
N B:GLY165 3.8 10.0 1.0
SD B:MET71 3.9 13.0 1.0
CA B:GLY165 4.0 11.3 1.0
CA B:TRP26 4.2 10.8 1.0
C43 B:BG7901 4.3 17.6 1.0
C B:HIS164 4.4 10.7 1.0
N B:TRP26 4.5 12.3 1.0
C B:GLY69 4.5 14.6 1.0
C47 B:BG7901 4.6 16.7 1.0
OG B:SER25 4.7 11.2 1.0
N B:HIS164 4.8 10.4 1.0
CE B:MET71 4.8 12.8 1.0
C66 B:BG7901 4.9 20.3 1.0
CA B:HIS164 4.9 12.5 1.0
CG B:TRP26 4.9 12.6 1.0
O B:HIS164 4.9 9.4 1.0
C41 B:BG7901 5.0 16.6 1.0

Fluorine binding site 5 out of 6 in 5qc9

Go back to Fluorine Binding Sites List in 5qc9
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:16.8
occ:1.00
 F58 B:BG7901 0.0 16.8 1.0
C54 B:BG7901 1.3 14.4 1.0
F56 B:BG7901 2.1 14.1 1.0
F60 B:BG7901 2.1 15.2 1.0
C45 B:BG7901 2.4 14.6 1.0
N B:HIS164 3.0 10.4 1.0
C44 B:BG7901 3.0 16.2 1.0
C62 B:BG7901 3.0 14.1 1.0
C B:HIS164 3.1 10.7 1.0
N B:GLY165 3.3 10.0 1.0
C B:ASN163 3.3 14.3 1.0
C46 B:BG7901 3.4 14.3 1.0
CA B:HIS164 3.4 12.5 1.0
O B:HIS164 3.5 9.4 1.0
CA B:ASN163 3.9 15.8 1.0
O B:ASN163 3.9 13.5 1.0
CA B:GLY165 3.9 11.3 1.0
N B:ASN163 4.0 11.2 1.0
CA B:GLY137 4.2 12.3 1.0
N64 B:BG7901 4.2 16.6 1.0
O B:HOH1202 4.2 21.9 1.0
C43 B:BG7901 4.3 17.6 1.0
CG2 B:VAL162 4.5 12.7 1.0
C47 B:BG7901 4.6 16.7 1.0
C B:VAL162 4.6 15.9 1.0
CB B:VAL162 4.8 13.7 1.0
CB B:HIS164 4.9 12.3 1.0
OG B:SER25 5.0 11.2 1.0
C41 B:BG7901 5.0 16.6 1.0
O B:VAL162 5.0 16.4 1.0

Fluorine binding site 6 out of 6 in 5qc9

Go back to Fluorine Binding Sites List in 5qc9
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:15.2
occ:1.00
 F60 B:BG7901 0.0 15.2 1.0
C54 B:BG7901 1.3 14.4 1.0
F56 B:BG7901 2.1 14.1 1.0
F58 B:BG7901 2.1 16.8 1.0
C45 B:BG7901 2.4 14.6 1.0
C46 B:BG7901 2.7 14.3 1.0
CA B:GLY165 3.0 11.3 1.0
SD B:MET71 3.2 13.0 1.0
N B:GLY165 3.3 10.0 1.0
CE B:MET71 3.4 12.8 1.0
CA B:GLY137 3.5 12.3 1.0
C44 B:BG7901 3.7 16.2 1.0
C B:HIS164 3.7 10.7 1.0
O B:HIS164 3.7 9.4 1.0
O B:VAL136 3.9 11.2 1.0
C47 B:BG7901 4.0 16.7 1.0
N B:GLY137 4.0 11.4 1.0
C B:VAL136 4.3 10.4 1.0
C62 B:BG7901 4.3 14.1 1.0
C B:GLY165 4.5 11.0 1.0
N B:HIS164 4.6 10.4 1.0
CA B:HIS164 4.7 12.5 1.0
C43 B:BG7901 4.8 17.6 1.0
N B:VAL166 4.9 9.6 1.0
C B:GLY137 4.9 10.0 1.0
C41 B:BG7901 4.9 16.6 1.0
CA B:TRP26 5.0 10.8 1.0
CG B:MET71 5.0 8.9 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: Thu Aug 1 13:01:21 2024

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