Fluorine in PDB 6qlw: Cathepsin-K in Complex with Miv-710

All present enzymatic activity of Cathepsin-K in Complex with Miv-710:
3.4.22.38;

The structure of Cathepsin-K in Complex with Miv-710, PDB code: 6qlw was solved by D.J.Derbyshire, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	74.47 / 2.00
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.727, 69.484, 78.680, 90.00, 100.89, 90.00
R / Rfree (%)	18 / 22.5

The structure of Cathepsin-K in Complex with Miv-710 also contains other interesting chemical elements:

Chlorine	(Cl)	11 atoms
Sodium	(Na)	2 atoms

The binding sites of Fluorine atom in the Cathepsin-K in Complex with Miv-710 (pdb code 6qlw). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Cathepsin-K in Complex with Miv-710, PDB code: 6qlw:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Cathepsin-K in Complex with Miv-710


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin-K in Complex with Miv-710 within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:17.5 occ:0.95 F2 A:J5T301 0.0 17.5 0.9 C17 A:J5T301 1.4 17.6 0.9 C16 A:J5T301 2.6 17.4 0.9 S1 A:J5T301 2.7 17.7 0.9 C6 A:J5T301 2.9 16.7 0.9 O A:GLU59 3.0 16.4 1.0 C5 A:J5T301 3.1 17.1 0.9 O A:HOH487 3.2 10.8 1.0 OD1 A:ASN60 3.5 15.7 1.0 CA A:ASN60 3.5 16.1 1.0 N3 A:J5T301 3.7 17.8 0.9 C18 A:J5T301 3.8 18.4 0.9 C A:GLU59 3.9 16.4 1.0 ND2 A:ASN70 4.1 12.4 1.0 N A:ASN60 4.1 16.3 1.0 C A:ASN60 4.1 16.4 1.0 C3 A:J5T301 4.2 16.4 0.9 CD2 A:TYR67 4.3 16.2 1.0 N A:ASP61 4.4 16.7 1.0 CG A:ASN60 4.4 15.5 1.0 C4 A:J5T301 4.4 16.9 0.9 CE2 A:TYR67 4.5 16.6 1.0 CB A:ASN60 4.5 15.8 1.0 CA A:GLY66 4.6 15.0 1.0 O A:GLY65 4.8 15.6 1.0 O A:ASN60 4.9 16.6 1.0

Fluorine binding site 2 out of 4 in the Cathepsin-K in Complex with Miv-710


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin-K in Complex with Miv-710 within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:17.1 occ:0.95 F2 B:J5T301 0.0 17.1 0.9 C17 B:J5T301 1.4 17.6 0.9 C16 B:J5T301 2.5 17.8 0.9 S1 B:J5T301 2.7 18.1 0.9 C6 B:J5T301 2.9 16.9 0.9 O B:GLU59 3.0 18.6 1.0 C5 B:J5T301 3.0 17.4 0.9 OD1 B:ASN60 3.4 17.6 1.0 CA B:ASN60 3.5 18.5 1.0 N3 B:J5T301 3.6 18.4 0.9 C18 B:J5T301 3.8 18.7 0.9 C B:GLU59 3.9 18.7 1.0 ND2 B:ASN70 4.1 14.5 1.0 N B:ASN60 4.1 18.5 1.0 C B:ASN60 4.1 19.3 1.0 C3 B:J5T301 4.2 16.7 0.9 N B:ASP61 4.3 19.6 1.0 CD2 B:TYR67 4.3 16.5 1.0 CG B:ASN60 4.3 17.5 1.0 C4 B:J5T301 4.3 17.6 0.9 CB B:ASN60 4.4 18.1 1.0 CA B:GLY66 4.4 16.7 1.0 CE2 B:TYR67 4.5 17.0 1.0 O B:GLY65 4.7 17.8 1.0 N B:TYR67 4.9 15.7 1.0 O B:ASN60 4.9 19.8 1.0 C B:GLY66 5.0 16.1 1.0

Fluorine binding site 3 out of 4 in the Cathepsin-K in Complex with Miv-710


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin-K in Complex with Miv-710 within 5.0Å range: probe atom residue distance (Å) B Occ C:F301 b:15.7 occ:0.95 F2 C:J5T301 0.0 15.7 0.9 C17 C:J5T301 1.4 15.9 0.9 C16 C:J5T301 2.5 16.0 0.9 S1 C:J5T301 2.8 16.3 0.9 C6 C:J5T301 2.9 15.4 0.9 O C:GLU59 3.0 17.7 1.0 C5 C:J5T301 3.0 15.7 0.9 O C:HOH499 3.3 16.0 1.0 OD1 C:ASN60 3.6 16.3 1.0 CA C:ASN60 3.6 17.0 1.0 N3 C:J5T301 3.6 16.4 0.9 C18 C:J5T301 3.8 16.7 0.9 C C:GLU59 3.9 17.6 1.0 C3 C:J5T301 4.1 15.1 0.9 C C:ASN60 4.2 17.4 1.0 ND2 C:ASN70 4.2 13.0 1.0 N C:ASN60 4.2 17.3 1.0 CD2 C:TYR67 4.2 15.6 1.0 N C:ASP61 4.3 17.6 1.0 C4 C:J5T301 4.3 15.7 0.9 CE2 C:TYR67 4.4 16.0 1.0 CG C:ASN60 4.4 16.2 1.0 CB C:ASN60 4.5 16.5 1.0 CA C:GLY66 4.6 15.3 1.0 O C:GLY65 4.8 16.5 1.0 O C:ASN60 4.9 17.4 1.0

Fluorine binding site 4 out of 4 in the Cathepsin-K in Complex with Miv-710


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Cathepsin-K in Complex with Miv-710 within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:16.7 occ:0.95 F2 D:J5T301 0.0 16.7 0.9 C17 D:J5T301 1.4 17.1 0.9 C16 D:J5T301 2.5 17.4 0.9 S1 D:J5T301 2.7 17.6 0.9 C6 D:J5T301 2.8 16.7 0.9 C5 D:J5T301 3.0 17.1 0.9 O D:GLU59 3.0 18.1 1.0 OD1 D:ASN60 3.4 16.5 1.0 CA D:ASN60 3.5 17.5 1.0 N3 D:J5T301 3.6 18.0 0.9 C18 D:J5T301 3.7 18.2 0.9 C D:GLU59 3.9 17.9 1.0 C3 D:J5T301 4.1 16.4 0.9 C D:ASN60 4.1 18.1 1.0 N D:ASN60 4.1 17.6 1.0 ND2 D:ASN70 4.2 14.3 1.0 N D:ASP61 4.2 18.5 1.0 C4 D:J5T301 4.2 17.3 0.9 CD2 D:TYR67 4.3 15.6 1.0 CG D:ASN60 4.3 16.6 1.0 CB D:ASN60 4.4 16.9 1.0 CA D:GLY66 4.4 15.4 1.0 CE2 D:TYR67 4.5 16.0 1.0 O D:GLY65 4.6 16.3 1.0 N D:TYR67 4.9 14.7 1.0 O D:ASN60 4.9 18.5 1.0 C D:GLY66 5.0 15.0 1.0

D.J.Derbyshire, D.J.Derbyshire. N/A N/A.