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Fluorine in PDB 2yj9: Cathepsin L with A Nitrile Inhibitor

Enzymatic activity of Cathepsin L with A Nitrile Inhibitor

All present enzymatic activity of Cathepsin L with A Nitrile Inhibitor:
3.4.22.15;

Protein crystallography data

The structure of Cathepsin L with A Nitrile Inhibitor, PDB code: 2yj9 was solved by D.W.Banner, J.M.Benz, W.Haap, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.43 / 1.35
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 45.992, 57.153, 76.589, 90.00, 90.00, 90.00
R / Rfree (%) 15.033 / 20.091

Other elements in 2yj9:

The structure of Cathepsin L with A Nitrile Inhibitor also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Cathepsin L with A Nitrile Inhibitor (pdb code 2yj9). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Cathepsin L with A Nitrile Inhibitor, PDB code: 2yj9:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 2yj9

Go back to Fluorine Binding Sites List in 2yj9
Fluorine binding site 1 out of 3 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:31.2
occ:1.00
F36 A:YJ91221 0.0 31.2 1.0
C35 A:YJ91221 1.3 22.5 1.0
F37 A:YJ91221 2.1 29.0 1.0
F38 A:YJ91221 2.1 31.1 1.0
C30 A:YJ91221 2.4 20.9 1.0
H31 A:YJ91221 2.4 18.6 1.0
HG3 A:GLU63 2.6 17.7 1.0
HA2 A:GLY68 2.7 12.9 1.0
C31 A:YJ91221 2.8 19.2 1.0
HB2 A:GLU63 3.1 17.4 1.0
HA A:ASN62 3.3 13.3 1.0
CG A:GLU63 3.3 17.5 1.0
O A:GLY61 3.4 16.9 1.0
H A:GLU63 3.4 14.1 1.0
O A:GLY67 3.5 14.2 1.0
CA A:GLY68 3.6 12.9 1.0
CD A:GLU63 3.6 26.2 1.0
C29 A:YJ91221 3.7 18.6 1.0
CB A:GLU63 3.7 17.4 1.0
N A:GLY68 3.7 14.1 1.0
C A:GLY67 3.7 14.4 1.0
N A:GLU63 3.7 14.3 1.0
OE2 A:GLU63 3.9 32.6 1.0
H29 A:YJ91221 4.0 19.0 1.0
HA3 A:GLY68 4.1 12.8 1.0
O A:HOH2101 4.1 36.6 1.0
C32 A:YJ91221 4.2 17.2 1.0
HG2 A:GLU63 4.2 18.5 1.0
CA A:ASN62 4.2 13.4 1.0
H A:GLY68 4.2 13.3 1.0
OE1 A:GLU63 4.2 32.4 1.0
C A:ASN62 4.2 13.4 1.0
CA A:GLU63 4.4 16.1 1.0
C A:GLY61 4.5 14.5 1.0
HB3 A:GLU63 4.5 17.8 1.0
HA3 A:GLY67 4.5 15.7 1.0
HE2 A:TYR72 4.5 17.6 1.0
C A:GLY68 4.6 11.7 1.0
CA A:GLY67 4.7 14.9 1.0
HD2 A:TYR72 4.7 17.1 1.0
H32 A:YJ91221 4.8 17.1 1.0
HG A:LEU69 4.8 15.7 1.0
C34 A:YJ91221 4.8 18.7 1.0
OD1 A:ASN62 4.9 13.9 1.0
N A:ASN62 4.9 15.8 1.0
H A:LEU69 4.9 12.2 1.0
HA A:GLU63 5.0 15.8 1.0

Fluorine binding site 2 out of 3 in 2yj9

Go back to Fluorine Binding Sites List in 2yj9
Fluorine binding site 2 out of 3 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:29.0
occ:1.00
F37 A:YJ91221 0.0 29.0 1.0
C35 A:YJ91221 1.3 22.5 1.0
F36 A:YJ91221 2.1 31.2 1.0
F38 A:YJ91221 2.1 31.1 1.0
C30 A:YJ91221 2.4 20.9 1.0
HE2 A:TYR72 2.7 17.6 1.0
H29 A:YJ91221 2.7 19.0 1.0
HA2 A:GLY68 2.9 12.9 1.0
C29 A:YJ91221 2.9 18.6 1.0
HG A:LEU69 3.1 15.7 1.0
O A:GLY61 3.2 16.9 1.0
HD2 A:TYR72 3.3 17.1 1.0
CE2 A:TYR72 3.4 18.0 1.0
C31 A:YJ91221 3.6 19.2 1.0
HA A:ASN62 3.6 13.3 1.0
O A:HOH2101 3.7 36.6 1.0
CD2 A:TYR72 3.7 17.7 1.0
CA A:GLY68 3.8 12.9 1.0
H31 A:YJ91221 3.8 18.6 1.0
CG A:LEU69 4.1 15.9 1.0
H A:LEU69 4.1 12.2 1.0
C A:GLY61 4.1 14.5 1.0
HG3 A:GLU63 4.1 17.7 1.0
C A:GLY68 4.2 11.7 1.0
N A:LEU69 4.3 13.5 1.0
C34 A:YJ91221 4.3 18.7 1.0
OD1 A:ASN62 4.4 13.9 1.0
HA3 A:GLY68 4.4 12.8 1.0
CD1 A:LEU69 4.5 19.3 1.0
CA A:ASN62 4.5 13.4 1.0
N A:GLY68 4.5 14.1 1.0
CZ A:TYR72 4.6 17.6 1.0
HB2 A:LEU69 4.6 13.8 1.0
N A:ASN62 4.7 15.8 1.0
C32 A:YJ91221 4.7 17.2 1.0
HA3 A:GLY61 4.8 16.4 1.0
CB A:LEU69 4.8 12.7 1.0
H A:GLU63 4.8 14.1 1.0
H A:GLY68 4.8 13.3 1.0
CD2 A:LEU69 4.9 18.5 1.0
O A:GLY68 4.9 12.1 1.0
OH A:TYR72 4.9 22.9 1.0
H34 A:YJ91221 5.0 18.9 1.0

Fluorine binding site 3 out of 3 in 2yj9

Go back to Fluorine Binding Sites List in 2yj9
Fluorine binding site 3 out of 3 in the Cathepsin L with A Nitrile Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Cathepsin L with A Nitrile Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1221

b:31.1
occ:1.00
F38 A:YJ91221 0.0 31.1 1.0
C35 A:YJ91221 1.3 22.5 1.0
F36 A:YJ91221 2.1 31.2 1.0
F37 A:YJ91221 2.1 29.0 1.0
C30 A:YJ91221 2.4 20.9 1.0
O A:HOH2101 3.1 36.6 1.0
C29 A:YJ91221 3.2 18.6 1.0
H29 A:YJ91221 3.2 19.0 1.0
C31 A:YJ91221 3.3 19.2 1.0
H31 A:YJ91221 3.4 18.6 1.0
OE2 A:GLU63 3.6 32.6 1.0
HG3 A:GLU63 3.6 17.7 1.0
O A:GLY61 3.8 16.9 1.0
CD A:GLU63 3.9 26.2 1.0
HE2 A:TYR72 4.1 17.6 1.0
CG A:GLU63 4.2 17.5 1.0
HA2 A:GLY68 4.4 12.9 1.0
C34 A:YJ91221 4.4 18.7 1.0
C32 A:YJ91221 4.5 17.2 1.0
OE1 A:GLU63 4.5 32.4 1.0
HB2 A:GLU63 4.7 17.4 1.0
HA A:ASN62 4.9 13.3 1.0
HG A:LEU69 4.9 15.7 1.0
CE2 A:TYR72 4.9 18.0 1.0
HG2 A:GLU63 5.0 18.5 1.0
C33 A:YJ91221 5.0 18.0 1.0

Reference:

L.A.Hardegger, B.Kuhn, B.Spinnler, L.Anselm, R.Ecabert, M.Stihle, B.Gsell, R.Thoma, J.Diez, J.M.Benz, J.Plancher, G.Hartmann, Y.Isshiki, K.Morikami, N.Shimma, W.Haap, D.W.Banner, F.Diederich. Halogen Bonding at the Active Sites of Human Cathepsin L and MEK1 Kinase: Efficient Interactions in Different Environments. Chemmedchem V. 6 2048 2011.
ISSN: ISSN 1860-7179
PubMed: 21898833
DOI: 10.1002/CMDC.201100353
Page generated: Sun Dec 13 11:42:20 2020

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