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Fluorine in PDB 5qc5: 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: 5qc5 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) 28.23 / 2.40
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 113.030, 37.000, 105.170, 90.00, 107.94, 90.00
R / Rfree (%) 18 / 25.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc5). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human Cathepsin-S with Bound Ligand, PDB code: 5qc5:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5qc5

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Fluorine binding site 1 out of 8 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:45.3
occ:1.00
 F13 A:BAJ901 0.0 45.3 1.0
C3 A:BAJ901 1.4 44.6 1.0
C4 A:BAJ901 2.3 36.6 1.0
C2 A:BAJ901 2.4 36.5 1.0
CD A:LYS64 3.0 44.9 1.0
CG A:LYS64 3.1 38.5 1.0
CE A:LYS64 3.3 52.2 1.0
O A:GLY68 3.4 35.8 1.0
O A:GLY62 3.5 37.6 1.0
CB A:LYS64 3.5 37.7 1.0
N A:LYS64 3.5 40.1 1.0
C5 A:BAJ901 3.6 37.8 1.0
C1 A:BAJ901 3.6 36.7 1.0
C A:GLY68 3.8 32.5 1.0
O A:HOH1039 4.0 40.5 1.0
C A:ASN63 4.1 42.3 1.0
CA A:ASN63 4.1 39.3 1.0
C6 A:BAJ901 4.1 42.8 1.0
CA A:LYS64 4.1 36.9 1.0
N A:GLY69 4.3 35.2 1.0
CA A:GLY68 4.4 35.1 1.0
O A:ASN67 4.4 38.7 1.0
C A:GLY62 4.4 38.3 1.0
CA A:GLY69 4.6 31.5 1.0
NZ A:LYS64 4.7 54.2 1.0
N A:ASN63 4.7 33.5 1.0
N A:GLY68 4.8 34.2 1.0
C A:ASN67 4.9 40.7 1.0
O A:ASN63 5.0 40.2 1.0

Fluorine binding site 2 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 2 out of 8 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:38.9
occ:1.00
 F36 A:BAJ901 0.0 38.9 1.0
C34 A:BAJ901 1.4 36.2 1.0
F40 A:BAJ901 2.2 37.8 1.0
F38 A:BAJ901 2.2 37.0 1.0
C27 A:BAJ901 2.4 33.8 1.0
C19 A:BAJ901 3.0 36.1 1.0
O A:HOH1006 3.0 30.5 1.0
C21 A:BAJ901 3.0 38.5 1.0
N17 A:BAJ901 3.2 35.1 1.0
O A:GLY69 3.2 33.7 1.0
CB A:TRP26 3.4 25.6 1.0
C26 A:BAJ901 3.5 32.1 1.0
N A:GLY165 3.9 25.8 1.0
SD A:MET71 4.0 27.0 1.0
CA A:TRP26 4.1 29.4 1.0
CA A:GLY165 4.1 25.8 1.0
C A:GLY69 4.3 30.8 1.0
C23 A:BAJ901 4.3 33.3 1.0
N A:TRP26 4.4 31.5 1.0
CG A:TRP26 4.4 27.5 1.0
C A:HIS164 4.5 26.9 1.0
OG A:SER25 4.5 29.1 1.0
C15 A:BAJ901 4.6 41.1 1.0
C25 A:BAJ901 4.6 34.1 1.0
CD1 A:TRP26 4.8 30.5 1.0
N A:HIS164 4.9 28.6 1.0
CA A:PHE70 4.9 33.4 1.0
CA A:HIS164 4.9 28.8 1.0
CE A:MET71 5.0 25.2 1.0
C24 A:BAJ901 5.0 33.5 1.0
N A:GLY69 5.0 35.2 1.0

Fluorine binding site 3 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 3 out of 8 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:37.0
occ:1.00
 F38 A:BAJ901 0.0 37.0 1.0
C34 A:BAJ901 1.3 36.2 1.0
F40 A:BAJ901 2.1 37.8 1.0
F36 A:BAJ901 2.2 38.9 1.0
C27 A:BAJ901 2.4 33.8 1.0
C A:HIS164 3.0 26.9 1.0
C21 A:BAJ901 3.0 38.5 1.0
N A:GLY165 3.0 25.8 1.0
C19 A:BAJ901 3.0 36.1 1.0
N A:HIS164 3.1 28.6 1.0
O A:HIS164 3.4 27.4 1.0
CA A:HIS164 3.4 28.8 1.0
C26 A:BAJ901 3.4 32.1 1.0
CA A:GLY165 3.5 25.8 1.0
C A:ASN163 3.6 32.1 1.0
N17 A:BAJ901 4.0 35.1 1.0
CA A:GLY137 4.0 26.7 1.0
O A:ASN163 4.0 30.2 1.0
O A:HOH1006 4.2 30.5 1.0
CA A:ASN163 4.2 32.6 1.0
N A:ASN163 4.3 33.3 1.0
C23 A:BAJ901 4.3 33.3 1.0
CG2 A:VAL162 4.6 23.6 1.0
C25 A:BAJ901 4.6 34.1 1.0
OG A:SER25 4.7 29.1 1.0
C A:VAL162 4.7 33.0 1.0
CB A:VAL162 4.9 28.5 1.0
CB A:HIS164 4.9 26.5 1.0
SD A:MET71 4.9 27.0 1.0
N A:VAL138 4.9 26.1 1.0
C A:GLY165 5.0 27.1 1.0
C24 A:BAJ901 5.0 33.5 1.0

Fluorine binding site 4 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 4 out of 8 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
A:F901

b:37.8
occ:1.00
 F40 A:BAJ901 0.0 37.8 1.0
C34 A:BAJ901 1.3 36.2 1.0
F38 A:BAJ901 2.1 37.0 1.0
F36 A:BAJ901 2.2 38.9 1.0
C27 A:BAJ901 2.4 33.8 1.0
C26 A:BAJ901 2.7 32.1 1.0
SD A:MET71 2.8 27.0 1.0
CA A:GLY165 3.1 25.8 1.0
CE A:MET71 3.1 25.2 1.0
N A:GLY165 3.5 25.8 1.0
C21 A:BAJ901 3.7 38.5 1.0
CA A:GLY137 3.9 26.7 1.0
C A:HIS164 4.0 26.9 1.0
O A:VAL136 4.1 25.7 1.0
C25 A:BAJ901 4.1 34.1 1.0
O A:HIS164 4.2 27.4 1.0
C19 A:BAJ901 4.3 36.1 1.0
N A:GLY137 4.3 27.6 1.0
CB A:TRP26 4.4 25.6 1.0
C A:VAL136 4.5 27.5 1.0
CA A:TRP26 4.5 29.4 1.0
C A:GLY165 4.5 27.1 1.0
CG A:MET71 4.6 22.1 1.0
C23 A:BAJ901 4.8 33.3 1.0
N A:VAL166 4.9 25.9 1.0
O A:GLY69 4.9 33.7 1.0
C24 A:BAJ901 5.0 33.5 1.0
N17 A:BAJ901 5.0 35.1 1.0

Fluorine binding site 5 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 5 out of 8 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:40.9
occ:0.50
 F13 B:BAJ901 0.0 40.9 0.5
C3 B:BAJ901 1.3 37.8 0.5
C4 B:BAJ901 2.3 35.0 0.5
C2 B:BAJ901 2.3 33.5 0.5
CD B:LYS64 3.0 45.4 1.0
CG B:LYS64 3.0 37.4 1.0
CB B:LYS64 3.3 34.9 1.0
CE B:LYS64 3.4 50.9 1.0
N B:LYS64 3.4 36.0 1.0
O B:GLY68 3.5 35.2 1.0
C5 B:BAJ901 3.6 37.2 0.5
C1 B:BAJ901 3.6 46.4 0.5
O B:GLY62 3.7 38.4 1.0
C B:GLY68 3.8 37.2 1.0
CA B:LYS64 3.9 38.9 1.0
C B:ASN63 4.0 37.3 1.0
O B:HOH1074 4.0 33.9 1.0
C6 B:BAJ901 4.1 43.7 0.5
CA B:ASN63 4.2 38.5 1.0
CA B:GLY68 4.2 35.8 1.0
O B:ASN67 4.2 37.0 1.0
N B:GLY69 4.4 33.0 1.0
C B:GLY62 4.6 33.6 1.0
N B:GLY68 4.6 33.9 1.0
C B:ASN67 4.6 35.0 1.0
CA B:GLY69 4.8 33.9 1.0
NZ B:LYS64 4.8 49.8 1.0
N B:ASN63 4.8 40.0 1.0
O B:ASN63 4.8 39.3 1.0
C B:LYS64 4.9 37.2 1.0

Fluorine binding site 6 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 6 out of 8 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:29.7
occ:1.00
 F36 B:BAJ901 0.0 29.7 1.0
C34 B:BAJ901 1.3 30.2 1.0
F40 B:BAJ901 2.1 31.7 1.0
F38 B:BAJ901 2.2 29.8 1.0
C27 B:BAJ901 2.4 35.0 1.0
C21 B:BAJ901 3.0 32.6 1.0
C19 B:BAJ901 3.1 34.8 1.0
O B:HOH1069 3.2 33.2 1.0
O B:GLY69 3.2 31.4 1.0
N17 B:BAJ901 3.3 43.7 0.5
C26 B:BAJ901 3.4 30.8 1.0
CB B:TRP26 3.5 22.4 1.0
N B:GLY165 3.9 20.8 1.0
SD B:MET71 4.1 21.6 1.0
CA B:TRP26 4.1 26.9 1.0
CA B:GLY165 4.2 23.6 1.0
C B:GLY69 4.3 32.1 1.0
C23 B:BAJ901 4.3 31.4 1.0
N B:TRP26 4.4 26.8 1.0
OG B:SER25 4.5 27.8 1.0
C B:HIS164 4.5 25.8 1.0
CG B:TRP26 4.6 30.2 1.0
C25 B:BAJ901 4.6 31.2 1.0
C15 B:BAJ901 4.7 44.6 0.5
N B:HIS164 4.8 25.5 1.0
CA B:HIS164 4.9 25.0 1.0
CE B:MET71 4.9 24.4 1.0
CA B:PHE70 4.9 27.6 1.0
N B:GLY69 4.9 33.0 1.0
CD1 B:TRP26 4.9 29.8 1.0
C B:ASN163 5.0 28.5 1.0
C24 B:BAJ901 5.0 34.6 1.0

Fluorine binding site 7 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 7 out of 8 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 7 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:29.8
occ:1.00
 F38 B:BAJ901 0.0 29.8 1.0
C34 B:BAJ901 1.3 30.2 1.0
F40 B:BAJ901 2.1 31.7 1.0
F36 B:BAJ901 2.2 29.7 1.0
C27 B:BAJ901 2.4 35.0 1.0
C21 B:BAJ901 3.0 32.6 1.0
N B:HIS164 3.0 25.5 1.0
C19 B:BAJ901 3.0 34.8 1.0
C B:HIS164 3.1 25.8 1.0
N B:GLY165 3.2 20.8 1.0
C26 B:BAJ901 3.4 30.8 1.0
CA B:HIS164 3.4 25.0 1.0
C B:ASN163 3.4 28.5 1.0
O B:HIS164 3.4 27.7 1.0
CA B:GLY165 3.7 23.6 1.0
CA B:GLY137 3.9 21.6 1.0
CA B:ASN163 4.0 30.3 1.0
O B:ASN163 4.0 29.8 1.0
N17 B:BAJ901 4.0 43.7 0.5
N B:ASN163 4.1 30.9 1.0
C23 B:BAJ901 4.3 31.4 1.0
CG2 B:VAL162 4.3 24.9 1.0
O B:HOH1069 4.3 33.2 1.0
C B:VAL162 4.5 33.0 1.0
C25 B:BAJ901 4.6 31.2 1.0
OG B:SER25 4.7 27.8 1.0
CB B:VAL162 4.7 27.4 1.0
O B:VAL162 4.9 29.0 1.0
N B:GLY137 4.9 22.0 1.0
N B:VAL138 4.9 26.6 1.0
CB B:HIS164 4.9 22.9 1.0
C24 B:BAJ901 4.9 34.6 1.0
C B:GLY137 5.0 25.6 1.0

Fluorine binding site 8 out of 8 in 5qc5

Go back to Fluorine Binding Sites List in 5qc5
Fluorine binding site 8 out of 8 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 8 of Crystal Structure of Human Cathepsin-S with Bound Ligand within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F901

b:31.7
occ:1.00
 F40 B:BAJ901 0.0 31.7 1.0
C34 B:BAJ901 1.3 30.2 1.0
F36 B:BAJ901 2.1 29.7 1.0
F38 B:BAJ901 2.1 29.8 1.0
C27 B:BAJ901 2.3 35.0 1.0
C26 B:BAJ901 2.7 30.8 1.0
SD B:MET71 3.0 21.6 1.0
CE B:MET71 3.2 24.4 1.0
CA B:GLY165 3.2 23.6 1.0
N B:GLY165 3.5 20.8 1.0
C21 B:BAJ901 3.7 32.6 1.0
CA B:GLY137 3.7 21.6 1.0
C B:HIS164 4.0 25.8 1.0
N B:GLY137 4.0 22.0 1.0
C25 B:BAJ901 4.1 31.2 1.0
O B:VAL136 4.1 22.4 1.0
O B:HIS164 4.2 27.7 1.0
C B:VAL136 4.3 26.3 1.0
C19 B:BAJ901 4.3 34.8 1.0
CB B:TRP26 4.6 22.4 1.0
C B:GLY165 4.6 26.6 1.0
CA B:TRP26 4.6 26.9 1.0
C23 B:BAJ901 4.7 31.4 1.0
CG B:MET71 4.8 22.0 1.0
O B:GLY69 4.9 31.4 1.0
N B:HIS164 4.9 25.5 1.0
C24 B:BAJ901 4.9 34.6 1.0
CA B:HIS164 4.9 25.0 1.0
N17 B:BAJ901 5.0 43.7 0.5

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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