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Fluorine in PDB 5qc6: 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: 5qc6 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) 34.09 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.078, 58.012, 58.931, 102.44, 107.58, 106.19
R / Rfree (%) 14.4 / 18.1

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc6). 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: 5qc6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5qc6

Go back to Fluorine Binding Sites List in 5qc6
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:15.0
occ:1.00
 F58 A:BCJ901 0.0 15.0 1.0
C53 A:BCJ901 1.3 15.2 1.0
F60 A:BCJ901 2.1 14.7 1.0
F62 A:BCJ901 2.1 13.0 1.0
C33 A:BCJ901 2.4 13.3 1.0
C34 A:BCJ901 3.1 15.3 1.0
O A:GLY69 3.2 15.1 1.0
O A:HOH1208 3.3 15.9 1.0
C32 A:BCJ901 3.3 11.5 1.0
S64 A:BCJ901 3.4 14.0 1.0
CB A:TRP26 3.5 10.6 1.0
SD A:MET71 3.7 13.1 1.0
N A:GLY165 3.9 12.1 1.0
CA A:GLY165 4.0 11.9 1.0
CA A:TRP26 4.1 11.0 1.0
O A:HOH1017 4.2 19.3 1.0
C A:GLY69 4.4 15.9 1.0
C35 A:BCJ901 4.4 9.9 1.0
C65 A:BCJ901 4.5 22.1 0.5
C A:HIS164 4.5 10.6 1.0
N A:TRP26 4.5 12.2 1.0
C31 A:BCJ901 4.5 12.7 1.0
CE A:MET71 4.6 11.3 1.0
C63 A:BCJ901 4.6 15.5 1.0
CG A:TRP26 4.7 14.0 1.0
O A:HOH1187 4.8 35.1 1.0
OG A:SER25 4.9 12.1 1.0
CA A:PHE70 4.9 12.5 1.0
N A:HIS164 4.9 12.5 1.0
CA A:HIS164 5.0 12.7 1.0
C20 A:BCJ901 5.0 12.5 1.0

Fluorine binding site 2 out of 6 in 5qc6

Go back to Fluorine Binding Sites List in 5qc6
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:14.7
occ:1.00
 F60 A:BCJ901 0.0 14.7 1.0
C53 A:BCJ901 1.3 15.2 1.0
F62 A:BCJ901 2.1 13.0 1.0
F58 A:BCJ901 2.1 15.0 1.0
C33 A:BCJ901 2.3 13.3 1.0
S64 A:BCJ901 2.8 14.0 1.0
C34 A:BCJ901 2.9 15.3 1.0
N A:HIS164 3.0 12.5 1.0
C A:HIS164 3.1 10.6 1.0
N A:GLY165 3.2 12.1 1.0
C A:ASN163 3.4 15.4 1.0
CA A:HIS164 3.4 12.7 1.0
O A:HIS164 3.5 12.0 1.0
C32 A:BCJ901 3.5 11.5 1.0
CA A:GLY165 3.8 11.9 1.0
CA A:ASN163 4.0 16.9 1.0
O A:ASN163 4.0 13.6 1.0
O A:HOH1208 4.2 15.9 1.0
N A:ASN163 4.2 10.3 1.0
C35 A:BCJ901 4.2 9.9 1.0
CA A:GLY137 4.3 11.0 1.0
CG2 A:VAL162 4.6 7.0 1.0
C63 A:BCJ901 4.6 15.5 1.0
O A:HOH1187 4.6 35.1 1.0
C31 A:BCJ901 4.7 12.7 1.0
C A:VAL162 4.7 17.2 1.0
O A:HOH1017 4.9 19.3 1.0
CB A:VAL162 4.9 11.1 1.0
CB A:HIS164 4.9 14.4 1.0
OG A:SER25 4.9 12.1 1.0
C20 A:BCJ901 5.0 12.5 1.0

Fluorine binding site 3 out of 6 in 5qc6

Go back to Fluorine Binding Sites List in 5qc6
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:13.0
occ:1.00
 F62 A:BCJ901 0.0 13.0 1.0
C53 A:BCJ901 1.3 15.2 1.0
F60 A:BCJ901 2.1 14.7 1.0
F58 A:BCJ901 2.1 15.0 1.0
C33 A:BCJ901 2.4 13.3 1.0
C32 A:BCJ901 2.7 11.5 1.0
CA A:GLY165 3.1 11.9 1.0
CE A:MET71 3.2 11.3 1.0
SD A:MET71 3.2 13.1 1.0
N A:GLY165 3.4 12.1 1.0
CA A:GLY137 3.5 11.0 1.0
C34 A:BCJ901 3.6 15.3 1.0
C A:HIS164 3.7 10.6 1.0
O A:HIS164 3.7 12.0 1.0
O A:VAL136 3.9 11.0 1.0
N A:GLY137 4.0 10.1 1.0
C31 A:BCJ901 4.1 12.7 1.0
C A:VAL136 4.2 9.8 1.0
S64 A:BCJ901 4.4 14.0 1.0
C A:GLY165 4.5 11.3 1.0
N A:HIS164 4.7 12.5 1.0
CA A:HIS164 4.7 12.7 1.0
C35 A:BCJ901 4.8 9.9 1.0
N A:VAL166 4.9 11.7 1.0
C A:GLY137 4.9 9.1 1.0
CB A:TRP26 4.9 10.6 1.0
C20 A:BCJ901 4.9 12.5 1.0
CG A:MET71 5.0 10.1 1.0
CA A:TRP26 5.0 11.0 1.0

Fluorine binding site 4 out of 6 in 5qc6

Go back to Fluorine Binding Sites List in 5qc6
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:14.0
occ:1.00
 F58 B:BCJ901 0.0 14.0 1.0
C53 B:BCJ901 1.3 12.4 1.0
F60 B:BCJ901 2.1 15.8 1.0
F62 B:BCJ901 2.1 12.5 1.0
C33 B:BCJ901 2.4 9.3 1.0
O B:GLY69 3.1 13.8 1.0
C34 B:BCJ901 3.1 12.8 1.0
O B:HOH1135 3.2 17.5 1.0
S64 B:BCJ901 3.3 13.0 1.0
C32 B:BCJ901 3.3 9.3 1.0
CB B:TRP26 3.7 12.4 1.0
SD B:MET71 3.9 8.4 1.0
N B:GLY165 4.0 9.1 1.0
O B:HOH1215 4.2 29.8 1.0
CA B:GLY165 4.2 9.1 1.0
C B:GLY69 4.2 13.8 1.0
CA B:TRP26 4.3 13.6 1.0
C65 B:BCJ901 4.4 21.8 0.5
C35 B:BCJ901 4.4 13.1 1.0
C B:HIS164 4.5 11.0 1.0
C31 B:BCJ901 4.6 11.2 1.0
C63 B:BCJ901 4.6 22.3 1.0
CE B:MET71 4.7 11.2 1.0
N B:TRP26 4.7 15.6 1.0
CA B:PHE70 4.8 11.9 1.0
CG B:TRP26 4.9 14.2 1.0
N B:HIS164 4.9 12.8 1.0
N B:PHE70 4.9 14.8 1.0
C20 B:BCJ901 5.0 13.6 1.0

Fluorine binding site 5 out of 6 in 5qc6

Go back to Fluorine Binding Sites List in 5qc6
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:15.8
occ:1.00
 F60 B:BCJ901 0.0 15.8 1.0
C53 B:BCJ901 1.3 12.4 1.0
F58 B:BCJ901 2.1 14.0 1.0
F62 B:BCJ901 2.1 12.5 1.0
C33 B:BCJ901 2.3 9.3 1.0
S64 B:BCJ901 2.8 13.0 1.0
C34 B:BCJ901 2.8 12.8 1.0
N B:HIS164 3.0 12.8 1.0
C B:HIS164 3.3 11.0 1.0
C B:ASN163 3.4 14.5 1.0
N B:GLY165 3.4 9.1 1.0
C32 B:BCJ901 3.5 9.3 1.0
CA B:HIS164 3.5 11.3 1.0
O B:HIS164 3.6 11.1 1.0
CA B:ASN163 3.9 13.0 1.0
O B:ASN163 3.9 12.9 1.0
CA B:GLY165 4.0 9.1 1.0
N B:ASN163 4.1 11.3 1.0
C35 B:BCJ901 4.2 13.1 1.0
O B:HOH1215 4.3 29.8 1.0
O B:HOH1135 4.3 17.5 1.0
CA B:GLY137 4.3 10.2 1.0
C63 B:BCJ901 4.5 22.3 1.0
C B:VAL162 4.5 13.5 1.0
CG2 B:VAL162 4.6 9.5 1.0
C31 B:BCJ901 4.7 11.2 1.0
O B:VAL162 4.8 9.1 1.0
CB B:VAL162 4.9 13.1 1.0
C20 B:BCJ901 5.0 13.6 1.0
O B:GLY69 5.0 13.8 1.0

Fluorine binding site 6 out of 6 in 5qc6

Go back to Fluorine Binding Sites List in 5qc6
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:12.5
occ:1.00
 F62 B:BCJ901 0.0 12.5 1.0
C53 B:BCJ901 1.3 12.4 1.0
F60 B:BCJ901 2.1 15.8 1.0
F58 B:BCJ901 2.1 14.0 1.0
C33 B:BCJ901 2.4 9.3 1.0
C32 B:BCJ901 2.8 9.3 1.0
CE B:MET71 3.2 11.2 1.0
SD B:MET71 3.2 8.4 1.0
CA B:GLY165 3.2 9.1 1.0
N B:GLY165 3.5 9.1 1.0
CA B:GLY137 3.5 10.2 1.0
C34 B:BCJ901 3.6 12.8 1.0
C B:HIS164 3.8 11.0 1.0
O B:HIS164 3.8 11.1 1.0
O B:VAL136 4.0 8.7 1.0
N B:GLY137 4.1 10.5 1.0
C31 B:BCJ901 4.1 11.2 1.0
C B:VAL136 4.3 9.4 1.0
S64 B:BCJ901 4.4 13.0 1.0
C B:GLY165 4.6 12.4 1.0
N B:HIS164 4.6 12.8 1.0
CA B:HIS164 4.7 11.3 1.0
C35 B:BCJ901 4.8 13.1 1.0
C B:GLY137 4.9 9.7 1.0
CG B:MET71 5.0 10.2 1.0
C20 B:BCJ901 5.0 13.6 1.0
O B:GLY69 5.0 13.8 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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