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Fluorine in PDB 5qc2: 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: 5qc2 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) 26.81 / 2.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 36.974, 53.635, 58.487, 70.60, 72.11, 73.58
R / Rfree (%) 14.2 / 21

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Cathepsin-S with Bound Ligand (pdb code 5qc2). 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: 5qc2:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:19.6
occ:1.00
 F13 A:BQP901 0.0 19.6 1.0
C4 A:BQP901 1.4 14.7 1.0
C3 A:BQP901 2.4 19.6 1.0
C5 A:BQP901 2.4 18.3 1.0
C6 A:BQP901 2.9 16.6 1.0
C2 A:BQP901 2.9 18.6 1.0
CG A:LYS64 3.2 21.3 1.0
C A:GLY68 3.4 18.7 1.0
O A:GLY68 3.4 15.9 1.0
N1 A:BQP901 3.5 23.8 1.0
N A:GLY69 3.7 18.4 1.0
CD A:LYS64 3.7 28.1 1.0
O A:GLY62 3.7 14.9 1.0
CA A:GLY68 3.9 18.4 1.0
CB A:LYS64 3.9 19.5 1.0
N A:LYS64 4.0 17.9 1.0
CA A:GLY69 4.0 17.1 1.0
O A:ASN67 4.1 26.5 1.0
CE A:LYS64 4.2 26.0 1.0
CA A:ASN63 4.3 19.7 1.0
C A:ASN63 4.4 22.9 1.0
N A:GLY68 4.5 19.7 1.0
O A:HOH1008 4.5 21.2 1.0
CA A:LYS64 4.6 18.4 1.0
C A:ASN67 4.7 23.0 1.0
C15 A:BQP901 4.7 17.1 1.0
C A:GLY62 4.8 17.6 1.0
C A:GLY69 4.9 17.1 1.0

Fluorine binding site 2 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:21.2
occ:1.00
 F47 A:BQP901 0.0 21.2 1.0
C33 A:BQP901 1.3 19.7 1.0
F48 A:BQP901 2.1 24.1 1.0
F49 A:BQP901 2.1 16.6 1.0
C21 A:BQP901 2.4 13.6 1.0
S19 A:BQP901 2.8 17.1 1.0
C26 A:BQP901 2.9 14.1 1.0
N A:HIS164 3.0 17.6 1.0
C A:HIS164 3.1 16.2 1.0
N A:GLY165 3.2 12.8 1.0
C A:ASN163 3.3 18.5 1.0
CA A:HIS164 3.3 16.3 1.0
O A:HIS164 3.5 16.2 1.0
C22 A:BQP901 3.5 15.0 1.0
O A:ASN163 3.7 18.3 1.0
CA A:GLY165 3.8 13.0 1.0
O A:HOH1143 3.9 16.6 1.0
CA A:ASN163 4.0 19.2 1.0
C25 A:BQP901 4.2 16.1 1.0
N A:ASN163 4.3 17.7 1.0
CA A:GLY137 4.4 15.5 1.0
C17 A:BQP901 4.6 16.7 1.0
OG A:SER25 4.7 14.5 1.0
C23 A:BQP901 4.7 15.3 1.0
CG2 A:VAL162 4.8 17.6 1.0
C A:VAL162 4.9 22.4 1.0
CB A:HIS164 4.9 16.4 1.0
C15 A:BQP901 5.0 17.1 1.0
C24 A:BQP901 5.0 16.0 1.0

Fluorine binding site 3 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:24.1
occ:1.00
 F48 A:BQP901 0.0 24.1 1.0
C33 A:BQP901 1.3 19.7 1.0
F47 A:BQP901 2.1 21.2 1.0
F49 A:BQP901 2.2 16.6 1.0
C21 A:BQP901 2.4 13.6 1.0
O A:HOH1143 3.0 16.6 1.0
C26 A:BQP901 3.2 14.1 1.0
C22 A:BQP901 3.3 15.0 1.0
O A:GLY69 3.4 22.4 1.0
S19 A:BQP901 3.5 17.1 1.0
CB A:TRP26 3.6 14.4 1.0
SD A:MET71 3.8 16.4 1.0
N A:GLY165 4.0 12.8 1.0
CA A:TRP26 4.1 15.3 1.0
CA A:GLY165 4.1 13.0 1.0
N A:TRP26 4.3 19.1 1.0
C15 A:BQP901 4.3 17.1 1.0
C25 A:BQP901 4.4 16.1 1.0
C A:HIS164 4.5 16.2 1.0
C23 A:BQP901 4.5 15.3 1.0
C A:GLY69 4.6 17.1 1.0
OG A:SER25 4.6 14.5 1.0
C17 A:BQP901 4.6 16.7 1.0
CG A:TRP26 4.8 17.9 1.0
CE A:MET71 4.8 12.3 1.0
C24 A:BQP901 5.0 16.0 1.0
CA A:HIS164 5.0 16.3 1.0
N A:HIS164 5.0 17.6 1.0

Fluorine binding site 4 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:16.6
occ:1.00
 F49 A:BQP901 0.0 16.6 1.0
C33 A:BQP901 1.3 19.7 1.0
F47 A:BQP901 2.1 21.2 1.0
F48 A:BQP901 2.2 24.1 1.0
C21 A:BQP901 2.4 13.6 1.0
C22 A:BQP901 2.7 15.0 1.0
CA A:GLY165 3.0 13.0 1.0
SD A:MET71 3.3 16.4 1.0
N A:GLY165 3.3 12.8 1.0
CE A:MET71 3.5 12.3 1.0
CA A:GLY137 3.6 15.5 1.0
C A:HIS164 3.6 16.2 1.0
C26 A:BQP901 3.7 14.1 1.0
O A:HIS164 3.7 16.2 1.0
O A:VAL136 3.9 15.5 1.0
N A:GLY137 4.0 17.1 1.0
C23 A:BQP901 4.1 15.3 1.0
C A:VAL136 4.3 15.6 1.0
S19 A:BQP901 4.5 17.1 1.0
C A:GLY165 4.5 15.5 1.0
CA A:HIS164 4.6 16.3 1.0
N A:HIS164 4.6 17.6 1.0
C25 A:BQP901 4.8 16.1 1.0
N A:VAL166 4.8 12.1 1.0
C24 A:BQP901 4.9 16.0 1.0
CA A:TRP26 4.9 15.3 1.0
C A:GLY137 4.9 17.1 1.0

Fluorine binding site 5 out of 8 in 5qc2

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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:21.7
occ:1.00
 F13 B:BQP901 0.0 21.7 1.0
C4 B:BQP901 1.4 16.8 1.0
C5 B:BQP901 2.4 17.5 1.0
C3 B:BQP901 2.4 19.9 1.0
C6 B:BQP901 2.9 17.8 1.0
C2 B:BQP901 2.9 17.3 1.0
C B:GLY68 3.3 17.9 1.0
O B:GLY68 3.4 19.4 1.0
CG B:LYS64 3.5 21.3 1.0
N1 B:BQP901 3.5 18.3 1.0
N B:GLY69 3.6 17.5 1.0
O B:GLY62 3.6 22.2 1.0
CE B:LYS64 3.8 34.3 1.0
N B:LYS64 3.8 22.3 1.0
CA B:GLY69 3.9 18.1 1.0
CA B:GLY68 3.9 18.0 1.0
CB B:LYS64 4.0 22.3 1.0
CA B:ASN63 4.1 21.3 1.0
CD B:LYS64 4.1 30.0 1.0
C B:ASN63 4.3 23.3 1.0
O B:ASN67 4.4 23.7 1.0
CA B:LYS64 4.5 21.6 1.0
N B:GLY68 4.6 16.0 1.0
C B:GLY62 4.6 21.0 1.0
C15 B:BQP901 4.6 16.1 1.0
O B:HOH1197 4.7 29.9 1.0
O B:HOH1076 4.7 24.5 1.0
C B:GLY69 4.7 21.6 1.0
C B:ASN67 4.8 19.8 1.0
N B:ASN63 4.8 17.3 1.0
OD1 B:ASN63 4.8 18.0 1.0

Fluorine binding site 6 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:22.3
occ:1.00
 F47 B:BQP901 0.0 22.3 1.0
C33 B:BQP901 1.3 20.8 1.0
F48 B:BQP901 2.1 20.1 1.0
F49 B:BQP901 2.2 18.0 1.0
C21 B:BQP901 2.4 16.5 1.0
N B:HIS164 2.9 16.4 1.0
S19 B:BQP901 2.9 19.4 1.0
C26 B:BQP901 2.9 15.7 1.0
C B:HIS164 3.2 14.3 1.0
C B:ASN163 3.2 18.3 1.0
CA B:HIS164 3.4 13.8 1.0
N B:GLY165 3.4 15.5 1.0
C22 B:BQP901 3.5 14.7 1.0
O B:HIS164 3.5 15.8 1.0
CA B:ASN163 3.8 16.9 1.0
O B:ASN163 3.8 20.9 1.0
N B:ASN163 3.9 17.8 1.0
CA B:GLY165 4.0 15.7 1.0
CA B:GLY137 4.0 12.6 1.0
CG2 B:VAL162 4.2 9.3 1.0
C25 B:BQP901 4.3 15.5 1.0
C B:VAL162 4.4 22.4 1.0
O B:HOH1162 4.4 21.9 1.0
CB B:VAL162 4.5 15.3 1.0
C23 B:BQP901 4.7 13.5 1.0
C17 B:BQP901 4.7 14.6 1.0
O B:VAL162 4.8 17.9 1.0
CB B:HIS164 4.9 13.4 1.0
N B:VAL138 4.9 14.1 1.0
C B:GLY137 5.0 16.4 1.0
C24 B:BQP901 5.0 16.7 1.0
O B:VAL138 5.0 16.0 1.0

Fluorine binding site 7 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:20.1
occ:1.00
 F48 B:BQP901 0.0 20.1 1.0
C33 B:BQP901 1.3 20.8 1.0
F49 B:BQP901 2.1 18.0 1.0
F47 B:BQP901 2.1 22.3 1.0
C21 B:BQP901 2.4 16.5 1.0
C26 B:BQP901 3.1 15.7 1.0
O B:HOH1162 3.2 21.9 1.0
S19 B:BQP901 3.3 19.4 1.0
C22 B:BQP901 3.3 14.7 1.0
O B:GLY69 3.6 19.1 1.0
N B:GLY165 3.9 15.5 1.0
CB B:TRP26 3.9 16.9 1.0
SD B:MET71 4.0 14.3 1.0
CA B:GLY165 4.1 15.7 1.0
C15 B:BQP901 4.3 16.1 1.0
C B:HIS164 4.4 14.3 1.0
C25 B:BQP901 4.4 15.5 1.0
CA B:TRP26 4.4 14.8 1.0
C17 B:BQP901 4.5 14.6 1.0
C23 B:BQP901 4.5 13.5 1.0
N B:HIS164 4.7 16.4 1.0
N B:TRP26 4.7 17.4 1.0
CA B:HIS164 4.8 13.8 1.0
C B:GLY69 4.8 21.6 1.0
C B:ASN163 4.9 18.3 1.0
O B:HIS164 4.9 15.8 1.0
OG B:SER25 4.9 12.9 1.0
CE B:MET71 5.0 14.3 1.0
C24 B:BQP901 5.0 16.7 1.0
O B:ASN163 5.0 20.9 1.0

Fluorine binding site 8 out of 8 in 5qc2

Go back to Fluorine Binding Sites List in 5qc2
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:18.0
occ:1.00
 F49 B:BQP901 0.0 18.0 1.0
C33 B:BQP901 1.3 20.8 1.0
F48 B:BQP901 2.1 20.1 1.0
F47 B:BQP901 2.2 22.3 1.0
C21 B:BQP901 2.4 16.5 1.0
C22 B:BQP901 2.7 14.7 1.0
CA B:GLY165 3.2 15.7 1.0
CA B:GLY137 3.3 12.6 1.0
SD B:MET71 3.3 14.3 1.0
CE B:MET71 3.5 14.3 1.0
N B:GLY165 3.5 15.5 1.0
C26 B:BQP901 3.7 15.7 1.0
C B:HIS164 3.8 14.3 1.0
N B:GLY137 3.8 12.1 1.0
O B:HIS164 3.8 15.8 1.0
O B:VAL136 3.9 14.1 1.0
C23 B:BQP901 4.1 13.5 1.0
C B:VAL136 4.1 11.8 1.0
S19 B:BQP901 4.5 19.4 1.0
N B:HIS164 4.6 16.4 1.0
C B:GLY165 4.6 14.0 1.0
C B:GLY137 4.7 16.4 1.0
CA B:HIS164 4.7 13.8 1.0
C25 B:BQP901 4.8 15.5 1.0
CG2 B:VAL162 4.8 9.3 1.0
C24 B:BQP901 5.0 16.7 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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