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

Enzymatic activity of Cathepsin-K in Complex with Miv-710

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

Protein crystallography data

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

Other elements in 6qlw:

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

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

Fluorine Binding Sites:

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 6qlw

Go back to Fluorine Binding Sites List in 6qlw
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 6qlw

Go back to Fluorine Binding Sites List in 6qlw
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 6qlw

Go back to Fluorine Binding Sites List in 6qlw
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 6qlw

Go back to Fluorine Binding Sites List in 6qlw
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

Reference:

D.J.Derbyshire, D.J.Derbyshire. N/A N/A.
Page generated: Sun Dec 13 13:09:00 2020

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