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Fluorine in PDB 5qcb: 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: 5qcb 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) 34.04 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 37.005, 58.694, 58.053, 102.18, 106.17, 107.48
R / Rfree (%) 19.4 / 25.6

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 5qcb

Go back to Fluorine Binding Sites List in 5qcb
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:6.2
occ:1.00
 F15 A:BHV901 0.0 6.2 1.0
C13 A:BHV901 1.3 11.9 1.0
F17 A:BHV901 2.1 14.8 1.0
F19 A:BHV901 2.2 14.1 1.0
C4 A:BHV901 2.4 8.3 1.0
C3 A:BHV901 3.0 9.1 1.0
C21 A:BHV901 3.0 10.8 1.0
O A:GLY69 3.2 9.7 1.0
C5 A:BHV901 3.4 8.2 1.0
N23 A:BHV901 3.5 13.1 1.0
SD A:MET71 3.8 4.9 1.0
CB A:TRP26 3.9 9.1 1.0
N A:GLY165 3.9 11.3 1.0
O A:HOH1172 3.9 20.6 1.0
CA A:GLY165 4.1 6.1 1.0
C2 A:BHV901 4.3 8.4 1.0
C A:GLY69 4.3 9.4 1.0
C A:HIS164 4.4 9.3 1.0
O A:HOH1150 4.4 26.6 1.0
CA A:TRP26 4.4 10.0 1.0
C6 A:BHV901 4.6 9.5 1.0
CE A:MET71 4.6 6.6 1.0
CA A:PHE70 4.6 7.6 1.0
N A:HIS164 4.8 8.7 1.0
N A:TRP26 4.8 7.0 1.0
O A:HIS164 4.8 11.5 1.0
C25 A:BHV901 4.9 16.4 1.0
CA A:HIS164 4.9 8.3 1.0
N A:PHE70 4.9 9.9 1.0
C1 A:BHV901 5.0 13.5 1.0
C A:ASN163 5.0 12.4 1.0

Fluorine binding site 2 out of 6 in 5qcb

Go back to Fluorine Binding Sites List in 5qcb
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:14.8
occ:1.00
 F17 A:BHV901 0.0 14.8 1.0
C13 A:BHV901 1.3 11.9 1.0
F19 A:BHV901 2.1 14.1 1.0
F15 A:BHV901 2.1 6.2 1.0
C4 A:BHV901 2.3 8.3 1.0
C5 A:BHV901 2.6 8.2 1.0
CE A:MET71 3.1 6.6 1.0
SD A:MET71 3.1 4.9 1.0
CA A:GLY137 3.3 8.8 1.0
CA A:GLY165 3.5 6.1 1.0
C3 A:BHV901 3.6 9.1 1.0
N A:GLY137 3.8 6.7 1.0
N A:GLY165 3.8 11.3 1.0
O A:HIS164 3.9 11.5 1.0
C6 A:BHV901 4.0 9.5 1.0
C A:HIS164 4.1 9.3 1.0
O A:VAL136 4.1 6.5 1.0
C A:VAL136 4.1 9.1 1.0
C21 A:BHV901 4.3 10.8 1.0
C2 A:BHV901 4.7 8.4 1.0
C A:GLY137 4.7 8.6 1.0
CG2 A:VAL162 4.8 10.2 1.0
C A:GLY165 4.8 8.7 1.0
O A:HOH1155 4.8 7.8 1.0
C1 A:BHV901 4.9 13.5 1.0
CG A:MET71 4.9 4.9 1.0
N A:HIS164 4.9 8.7 1.0

Fluorine binding site 3 out of 6 in 5qcb

Go back to Fluorine Binding Sites List in 5qcb
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:14.1
occ:1.00
 F19 A:BHV901 0.0 14.1 1.0
C13 A:BHV901 1.3 11.9 1.0
F17 A:BHV901 2.1 14.8 1.0
F15 A:BHV901 2.2 6.2 1.0
C4 A:BHV901 2.3 8.3 1.0
C3 A:BHV901 3.0 9.1 1.0
C21 A:BHV901 3.0 10.8 1.0
N A:HIS164 3.1 8.7 1.0
C A:HIS164 3.3 9.3 1.0
C5 A:BHV901 3.4 8.2 1.0
O A:HIS164 3.4 11.5 1.0
N A:GLY165 3.5 11.3 1.0
C A:ASN163 3.5 12.4 1.0
CA A:HIS164 3.7 8.3 1.0
CA A:GLY137 3.8 8.8 1.0
N A:ASN163 3.9 10.4 1.0
CA A:ASN163 3.9 12.7 1.0
CA A:GLY165 4.0 6.1 1.0
CG2 A:VAL162 4.0 10.2 1.0
N23 A:BHV901 4.2 13.1 1.0
O A:ASN163 4.3 13.4 1.0
C2 A:BHV901 4.3 8.4 1.0
C A:VAL162 4.3 9.8 1.0
CB A:VAL162 4.3 11.2 1.0
C6 A:BHV901 4.5 9.5 1.0
O A:VAL162 4.6 11.9 1.0
N A:VAL138 4.7 8.1 1.0
C A:GLY137 4.7 8.6 1.0
O A:HOH1172 4.8 20.6 1.0
N A:GLY137 4.8 6.7 1.0
CA A:VAL162 4.9 12.7 1.0
C1 A:BHV901 4.9 13.5 1.0

Fluorine binding site 4 out of 6 in 5qcb

Go back to Fluorine Binding Sites List in 5qcb
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:14.4
occ:1.00
 F15 B:BHV901 0.0 14.4 1.0
C13 B:BHV901 1.4 14.7 1.0
F19 B:BHV901 2.2 14.4 1.0
F17 B:BHV901 2.2 12.8 1.0
C4 B:BHV901 2.4 11.8 1.0
C21 B:BHV901 3.0 11.6 1.0
C3 B:BHV901 3.0 12.6 1.0
O B:GLY69 3.2 18.0 1.0
N23 B:BHV901 3.4 10.3 1.0
C5 B:BHV901 3.5 12.3 1.0
N B:GLY165 3.9 8.9 1.0
CB B:TRP26 3.9 11.1 1.0
SD B:MET71 4.1 12.7 1.0
CA B:GLY165 4.1 10.8 1.0
C B:GLY69 4.3 16.0 1.0
C2 B:BHV901 4.3 12.3 1.0
CA B:TRP26 4.4 6.5 1.0
C B:HIS164 4.4 8.4 1.0
N B:TRP26 4.7 11.8 1.0
C6 B:BHV901 4.7 12.5 1.0
C25 B:BHV901 4.7 22.4 1.0
N B:HIS164 4.8 8.4 1.0
CA B:PHE70 4.8 9.4 1.0
CA B:HIS164 4.9 8.9 1.0
O B:HIS164 4.9 8.7 1.0
C B:ASN163 4.9 12.5 1.0
OG B:SER25 5.0 8.2 1.0
CE B:MET71 5.0 10.1 1.0
N B:PHE70 5.0 14.3 1.0

Fluorine binding site 5 out of 6 in 5qcb

Go back to Fluorine Binding Sites List in 5qcb
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:12.8
occ:1.00
 F17 B:BHV901 0.0 12.8 1.0
C13 B:BHV901 1.4 14.7 1.0
F19 B:BHV901 2.2 14.4 1.0
F15 B:BHV901 2.2 14.4 1.0
C4 B:BHV901 2.4 11.8 1.0
C5 B:BHV901 2.7 12.3 1.0
SD B:MET71 3.1 12.7 1.0
CA B:GLY165 3.2 10.8 1.0
CE B:MET71 3.3 10.1 1.0
CA B:GLY137 3.5 7.0 1.0
N B:GLY165 3.6 8.9 1.0
C3 B:BHV901 3.7 12.6 1.0
O B:HIS164 3.8 8.7 1.0
O B:VAL136 3.9 10.1 1.0
C B:HIS164 3.9 8.4 1.0
N B:GLY137 3.9 10.5 1.0
C6 B:BHV901 4.1 12.5 1.0
C B:VAL136 4.2 8.2 1.0
C21 B:BHV901 4.3 11.6 1.0
C B:GLY165 4.6 7.3 1.0
C2 B:BHV901 4.8 12.3 1.0
N B:HIS164 4.9 8.4 1.0
C B:GLY137 4.9 7.2 1.0
CG B:MET71 4.9 8.4 1.0
CA B:HIS164 4.9 8.9 1.0
N B:VAL166 4.9 8.2 1.0
C1 B:BHV901 5.0 10.5 1.0
CG2 B:VAL162 5.0 11.7 1.0
O B:GLY69 5.0 18.0 1.0

Fluorine binding site 6 out of 6 in 5qcb

Go back to Fluorine Binding Sites List in 5qcb
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:14.4
occ:1.00
 F19 B:BHV901 0.0 14.4 1.0
C13 B:BHV901 1.3 14.7 1.0
F17 B:BHV901 2.2 12.8 1.0
F15 B:BHV901 2.2 14.4 1.0
C4 B:BHV901 2.4 11.8 1.0
C3 B:BHV901 3.0 12.6 1.0
N B:HIS164 3.1 8.4 1.0
C21 B:BHV901 3.1 11.6 1.0
C B:HIS164 3.1 8.4 1.0
O B:HIS164 3.3 8.7 1.0
N B:GLY165 3.3 8.9 1.0
C5 B:BHV901 3.4 12.3 1.0
C B:ASN163 3.4 12.5 1.0
CA B:HIS164 3.5 8.9 1.0
CA B:GLY165 3.9 10.8 1.0
CA B:ASN163 3.9 7.6 1.0
CA B:GLY137 3.9 7.0 1.0
N B:ASN163 3.9 9.8 1.0
O B:ASN163 4.1 7.3 1.0
CG2 B:VAL162 4.1 11.7 1.0
N23 B:BHV901 4.3 10.3 1.0
C2 B:BHV901 4.3 12.3 1.0
C B:VAL162 4.5 12.9 1.0
CB B:VAL162 4.5 9.3 1.0
C6 B:BHV901 4.6 12.5 1.0
N B:VAL138 4.8 6.6 1.0
C B:GLY137 4.9 7.2 1.0
O B:VAL162 4.9 11.2 1.0
N B:GLY137 4.9 10.5 1.0
O B:VAL138 5.0 10.7 1.0
C1 B:BHV901 5.0 10.5 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: Thu Aug 1 13:01:21 2024

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