Fluorine in PDB 6h23: Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule

All present enzymatic activity of Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule:
3.4.21.92;

The structure of Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule, PDB code: 6h23 was solved by L.M.Kick, S.A.Sieber, S.Schneider, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	42.34 / 3.09
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	115.504, 97.153, 127.249, 90.00, 93.53, 90.00
R / Rfree (%)	21.5 / 26.1

The structure of Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule also contains other interesting chemical elements:

Chlorine

(Cl)

27 atoms

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 20; Page 3, Binding sites: 21 - 27;

Binding sites:

The binding sites of Fluorine atom in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule (pdb code 6h23). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 27 binding sites of Fluorine where determined in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule, PDB code: 6h23:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Fluorine binding site 1 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:82.7 occ:0.43 F22 A:FJT301 0.0 82.7 0.4 F22 A:FJT301 0.9 82.4 0.3 C19 A:FJT301 1.2 83.3 0.3 C19 A:FJT301 1.4 83.5 0.4 C20 A:FJT301 1.7 83.2 0.3 C20 A:FJT301 2.4 84.1 0.4 C18 A:FJT301 2.4 83.5 0.4 C18 A:FJT301 2.5 83.3 0.3 C21 A:FJT301 3.0 84.8 0.3 CG2 B:VAL148 3.0 73.4 1.0 C17 A:FJT301 3.6 83.9 0.3 C21 A:FJT301 3.6 84.9 0.4 C17 A:FJT301 3.6 84.0 0.4 C16 A:FJT301 3.8 84.8 0.3 CG2 A:ILE100 3.8 68.3 1.0 C16 A:FJT301 4.1 84.5 0.4 OG1 A:THR135 4.2 66.2 1.0 CB B:VAL148 4.2 67.7 1.0 CD1 A:LEU104 4.3 79.0 1.0 CG1 B:VAL148 4.5 69.9 1.0 CD1 B:LEU170 4.5 67.6 1.0 CD1 A:ILE100 4.8 57.9 1.0

Fluorine binding site 2 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ A:F301 b:82.4 occ:0.34 F22 A:FJT301 0.0 82.4 0.3 F22 A:FJT301 0.9 82.7 0.4 C19 A:FJT301 1.4 83.3 0.3 C19 A:FJT301 1.7 83.5 0.4 C18 A:FJT301 2.2 83.5 0.4 C18 A:FJT301 2.4 83.3 0.3 C20 A:FJT301 2.4 83.2 0.3 C20 A:FJT301 3.0 84.1 0.4 CG2 B:VAL148 3.1 73.4 1.0 C17 A:FJT301 3.6 84.0 0.4 C21 A:FJT301 3.6 84.8 0.3 C17 A:FJT301 3.6 83.9 0.3 CG2 A:ILE100 3.7 68.3 1.0 CB B:VAL148 4.0 67.7 1.0 C16 A:FJT301 4.1 84.8 0.3 C21 A:FJT301 4.1 84.9 0.4 CD1 A:LEU104 4.3 79.0 1.0 CG1 B:VAL148 4.3 69.9 1.0 C16 A:FJT301 4.3 84.5 0.4 CB B:ALA118 4.4 50.0 1.0 CD1 A:ILE100 4.7 57.9 1.0 OG1 A:THR135 4.8 66.2 1.0 CL1 A:FJT301 4.8 89.5 0.4

Fluorine binding site 3 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:81.4 occ:0.38 F22 B:FJT301 0.0 81.4 0.4 F22 B:FJT301 0.7 82.2 0.5 C19 B:FJT301 1.4 85.2 0.4 C19 B:FJT301 1.9 86.6 0.5 C20 B:FJT301 2.4 86.3 0.4 C18 B:FJT301 2.4 89.1 0.4 C18 B:FJT301 2.8 89.8 0.5 C20 B:FJT301 2.9 88.5 0.5 CG2 B:ILE100 3.1 67.6 1.0 OG1 B:THR135 3.5 64.5 1.0 CG2 C:VAL148 3.6 68.5 1.0 C21 B:FJT301 3.6 90.1 0.4 C17 B:FJT301 3.6 90.7 0.4 CB C:VAL148 3.9 65.8 1.0 CG1 C:VAL148 4.0 67.3 1.0 CD1 B:ILE100 4.0 62.1 1.0 C16 B:FJT301 4.1 91.2 0.4 C17 B:FJT301 4.1 91.3 0.5 C21 B:FJT301 4.2 91.5 0.5 CB B:ILE100 4.4 71.5 1.0 CG1 B:ILE100 4.5 64.9 1.0 CD1 C:LEU170 4.5 66.8 1.0 CG2 B:THR135 4.5 68.0 1.0 CB B:THR135 4.6 65.8 1.0 C16 B:FJT301 4.7 91.7 0.5 CD1 B:LEU104 4.9 88.9 1.0

Fluorine binding site 4 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ B:F301 b:82.2 occ:0.46 F22 B:FJT301 0.0 82.2 0.5 F22 B:FJT301 0.7 81.4 0.4 C19 B:FJT301 0.9 85.2 0.4 C19 B:FJT301 1.4 86.6 0.5 C20 B:FJT301 1.9 86.3 0.4 C18 B:FJT301 1.9 89.1 0.4 C18 B:FJT301 2.4 89.8 0.5 C20 B:FJT301 2.4 88.5 0.5 C21 B:FJT301 3.1 90.1 0.4 C17 B:FJT301 3.1 90.7 0.4 C16 B:FJT301 3.6 91.2 0.4 C17 B:FJT301 3.6 91.3 0.5 C21 B:FJT301 3.6 91.5 0.5 CG2 C:VAL148 3.7 68.5 1.0 CB C:VAL148 3.8 65.8 1.0 CG2 B:ILE100 3.8 67.6 1.0 OG1 B:THR135 3.9 64.5 1.0 CG1 C:VAL148 4.1 67.3 1.0 C16 B:FJT301 4.1 91.7 0.5 CD1 C:LEU170 4.2 66.8 1.0 CL1 B:FJT301 4.7 95.5 0.4 CD1 B:ILE100 4.7 62.1 1.0 CG2 B:THR135 4.9 68.0 1.0 CB B:THR135 5.0 65.8 1.0

Fluorine binding site 5 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ D:F301 b:74.4 occ:0.80 F22 D:FJT301 0.0 74.4 0.8 C19 D:FJT301 1.4 71.5 0.8 C18 D:FJT301 2.4 71.6 0.8 C20 D:FJT301 2.4 73.0 0.8 CG2 C:ILE100 3.6 62.4 1.0 C17 D:FJT301 3.6 76.5 0.8 C21 D:FJT301 3.6 77.8 0.8 CG2 D:VAL148 3.7 60.1 1.0 CB D:VAL148 3.7 56.5 1.0 OG1 C:THR135 3.8 62.3 1.0 CG1 D:VAL148 3.8 59.1 1.0 C16 D:FJT301 4.1 77.2 0.8 CD1 C:ILE100 4.4 54.7 1.0 CD1 D:LEU170 4.4 59.7 1.0 CG2 C:THR135 4.8 69.2 1.0 CB C:ILE100 4.8 64.5 1.0 CB C:THR135 4.9 65.0 1.0 CG1 C:ILE100 4.9 57.8 1.0 CD1 C:LEU104 5.0 79.6 1.0

Fluorine binding site 6 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ D:F302 b:68.3 occ:0.44 F22 D:FJT302 0.0 68.3 0.4 F22 D:FJT302 0.3 68.2 0.5 C19 D:FJT302 1.4 72.1 0.4 C19 D:FJT302 1.4 72.0 0.5 C20 D:FJT302 2.3 72.5 0.5 C18 D:FJT302 2.4 73.9 0.4 C20 D:FJT302 2.4 72.4 0.4 C18 D:FJT302 2.6 73.8 0.5 C21 D:FJT302 3.6 74.9 0.5 C21 D:FJT302 3.6 75.1 0.4 C17 D:FJT302 3.6 76.5 0.4 CG2 D:ILE100 3.7 60.8 1.0 C17 D:FJT302 3.8 76.1 0.5 CG2 E:VAL148 3.8 62.8 1.0 OG1 D:THR135 3.9 58.7 1.0 CB E:VAL148 3.9 55.5 1.0 C16 D:FJT302 4.1 76.4 0.4 CG1 E:VAL148 4.1 58.5 1.0 C16 D:FJT302 4.2 76.3 0.5 CD1 E:LEU170 4.3 57.9 1.0 CD1 D:ILE100 4.5 62.0 1.0 CD1 D:LEU104 4.7 71.6 1.0 CG2 D:THR135 4.9 57.4 1.0 CB D:ILE100 4.9 55.6 1.0 CG1 D:ILE100 5.0 52.5 1.0

Fluorine binding site 7 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ D:F302 b:68.2 occ:0.49 F22 D:FJT302 0.0 68.2 0.5 F22 D:FJT302 0.3 68.3 0.4 C19 D:FJT302 1.3 72.1 0.4 C19 D:FJT302 1.4 72.0 0.5 C18 D:FJT302 2.2 73.9 0.4 C18 D:FJT302 2.4 73.8 0.5 C20 D:FJT302 2.4 72.5 0.5 C20 D:FJT302 2.5 72.4 0.4 C17 D:FJT302 3.5 76.5 0.4 C17 D:FJT302 3.6 76.1 0.5 C21 D:FJT302 3.6 74.9 0.5 C21 D:FJT302 3.7 75.1 0.4 CG2 D:ILE100 3.7 60.8 1.0 CB E:VAL148 4.0 55.5 1.0 CG2 E:VAL148 4.0 62.8 1.0 C16 D:FJT302 4.1 76.4 0.4 CG1 E:VAL148 4.1 58.5 1.0 C16 D:FJT302 4.1 76.3 0.5 OG1 D:THR135 4.1 58.7 1.0 CD1 E:LEU170 4.5 57.9 1.0 CD1 D:LEU104 4.6 71.6 1.0 CD1 D:ILE100 4.6 62.0 1.0 CL1 D:FJT302 4.9 78.5 0.4 CB D:ILE100 5.0 55.6 1.0 CB E:ALA118 5.0 50.0 1.0

Fluorine binding site 8 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


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 the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ E:F301 b:66.1 occ:0.36 F22 E:FJT301 0.0 66.1 0.4 C19 E:FJT301 0.8 66.8 0.5 F22 E:FJT301 1.0 62.7 0.5 C19 E:FJT301 1.4 67.4 0.4 C20 E:FJT301 1.4 66.9 0.5 C18 E:FJT301 2.2 67.8 0.5 C20 E:FJT301 2.4 67.2 0.4 C18 E:FJT301 2.4 67.6 0.4 C21 E:FJT301 2.7 67.2 0.5 C17 E:FJT301 3.2 69.7 0.5 CG2 F:VAL148 3.3 64.8 1.0 C16 E:FJT301 3.4 69.3 0.5 C21 E:FJT301 3.6 68.3 0.4 C17 E:FJT301 3.7 69.6 0.4 CG2 E:ILE100 4.1 55.8 1.0 OG1 E:THR135 4.1 50.8 1.0 C16 E:FJT301 4.1 70.3 0.4 CD1 F:LEU170 4.3 62.4 1.0 CD1 E:LEU104 4.5 70.6 1.0 CB F:VAL148 4.5 62.8 1.0 CG1 F:VAL148 4.8 62.4 1.0 CL1 E:FJT301 4.8 67.9 0.5 C15 E:FJT301 4.9 72.2 0.5 CG2 E:THR135 5.0 50.7 1.0

Fluorine binding site 9 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 9 of Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ E:F301 b:62.7 occ:0.47 F22 E:FJT301 0.0 62.7 0.5 F22 E:FJT301 1.0 66.1 0.4 C19 E:FJT301 1.4 66.8 0.5 C19 E:FJT301 2.0 67.4 0.4 C18 E:FJT301 2.4 67.8 0.5 C20 E:FJT301 2.4 66.9 0.5 C20 E:FJT301 2.4 67.2 0.4 CG2 F:VAL148 3.1 64.8 1.0 C18 E:FJT301 3.2 67.6 0.4 CG2 E:ILE100 3.5 55.8 1.0 C21 E:FJT301 3.6 67.2 0.5 C17 E:FJT301 3.7 69.7 0.5 C21 E:FJT301 3.8 68.3 0.4 CB F:VAL148 4.1 62.8 1.0 OG1 E:THR135 4.1 50.8 1.0 CG1 F:VAL148 4.1 62.4 1.0 C16 E:FJT301 4.1 69.3 0.5 CD1 E:ILE100 4.3 49.6 1.0 C17 E:FJT301 4.4 69.6 0.4 CD1 E:LEU104 4.5 70.6 1.0 C16 E:FJT301 4.6 70.3 0.4 CB E:ILE100 4.7 56.5 1.0 CD1 F:LEU170 4.8 62.4 1.0 CG1 E:ILE100 4.8 53.9 1.0 CB F:ALA118 4.9 50.0 1.0

Fluorine binding site 10 out of 27 in the Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 10 of Crystal Structure of the Hclpp Y118A Mutant with An Activating Small Molecule within 5.0Å range: probe atom residue distance (Å) B Occ F:F301 b:70.9 occ:0.47 F22 F:FJT301 0.0 70.9 0.5 F22 F:FJT301 0.4 71.2 0.4 C19 F:FJT301 1.4 74.1 0.5 C19 F:FJT301 1.6 73.9 0.4 C20 F:FJT301 2.4 76.8 0.5 C18 F:FJT301 2.4 73.5 0.5 C20 F:FJT301 2.6 73.7 0.4 C18 F:FJT301 2.6 76.8 0.4 CG2 G:VAL148 3.2 64.4 1.0 C17 F:FJT301 3.6 75.6 0.5 C21 F:FJT301 3.6 77.8 0.5 OG1 F:THR135 3.8 47.6 1.0 CG2 F:ILE100 3.8 50.5 1.0 C21 F:FJT301 3.8 76.1 0.4 C17 F:FJT301 3.9 77.5 0.4 C16 F:FJT301 4.1 76.8 0.5 CB G:VAL148 4.2 55.0 1.0 C16 F:FJT301 4.4 77.3 0.4 CD1 G:LEU170 4.4 62.6 1.0 CG1 G:VAL148 4.4 56.9 1.0 CD1 F:LEU104 4.5 66.8 1.0 CD1 F:ILE100 4.6 51.5 1.0 CG2 F:THR135 4.7 53.2 1.0 CB F:THR135 4.8 54.2 1.0

M.Stahl, V.S.Korotkov, D.Balogh, L.M.Kick, M.Gersch, A.Pahl, P.Kielkowski, K.Richter, S.Schneider, S.A.Sieber. Selective Activation of Human Caseinolytic Protease P (Clpp). Angew. Chem. Int. Ed. Engl. V. 57 14602 2018.
ISSN: ESSN 1521-3773
PubMed: 30129683
DOI: 10.1002/ANIE.201808189