Fluorine in PDB 7qmk: Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)

Enzymatic activity of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)

All present enzymatic activity of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12), PDB code: 7qmk was solved by C.Y.Huang, S.Aumonier, M.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 35.24 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.81, 73.971, 53.448, 90, 109.62, 90
R / Rfree (%) 16.5 / 19.4

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) (pdb code 7qmk). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12), PDB code: 7qmk:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7qmk

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Fluorine binding site 1 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:56.8
occ:0.72
 F08 A:U1H2601 0.0 56.8 0.7
C07 A:U1H2601 1.4 58.1 0.7
F10 A:U1H2601 2.2 60.8 0.7
F09 A:U1H2601 2.2 53.3 0.7
C06 A:U1H2601 2.4 42.9 0.7
C05 A:U1H2601 2.9 45.9 0.7
CG2 A:ILE302 3.2 36.6 1.0
C11 A:U1H2601 3.5 51.6 0.7
CD1 A:ILE304 3.6 27.2 1.0
CG2 A:ILE300 4.2 39.0 1.0
C04 A:U1H2601 4.2 33.2 0.7
CG1 A:ILE304 4.2 20.2 1.0
C1 A:DMS2604 4.4 57.0 0.8
CD1 A:ILE217 4.6 25.8 1.0
C12 A:U1H2601 4.6 39.6 0.7
CB A:ILE302 4.6 29.3 1.0
C03 A:U1H2601 4.9 37.5 0.7

Fluorine binding site 2 out of 6 in 7qmk

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Fluorine binding site 2 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:53.3
occ:0.72
 F09 A:U1H2601 0.0 53.3 0.7
C07 A:U1H2601 1.4 58.1 0.7
F08 A:U1H2601 2.2 56.8 0.7
F10 A:U1H2601 2.2 60.8 0.7
C06 A:U1H2601 2.4 42.9 0.7
C11 A:U1H2601 2.7 51.6 0.7
C1 A:DMS2604 3.1 57.0 0.8
CA A:GLY80 3.3 55.4 1.0
C05 A:U1H2601 3.6 45.9 0.7
CG2 A:ILE300 3.9 39.0 1.0
C12 A:U1H2601 4.1 39.6 0.7
N A:GLY80 4.2 48.5 1.0
C A:GLY80 4.3 54.9 1.0
CD1 A:ILE304 4.3 27.2 1.0
O A:GLY80 4.5 52.3 1.0
S A:DMS2604 4.6 64.9 0.8
C04 A:U1H2601 4.8 33.2 0.7
CG2 A:ILE302 4.8 36.6 1.0
C03 A:U1H2601 4.9 37.5 0.7

Fluorine binding site 3 out of 6 in 7qmk

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Fluorine binding site 3 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:60.8
occ:0.72
 F10 A:U1H2601 0.0 60.8 0.7
C07 A:U1H2601 1.4 58.1 0.7
F08 A:U1H2601 2.2 56.8 0.7
F09 A:U1H2601 2.2 53.3 0.7
C06 A:U1H2601 2.3 42.9 0.7
C05 A:U1H2601 3.0 45.9 0.7
C11 A:U1H2601 3.4 51.6 0.7
C1 A:DMS2605 3.9 47.5 0.8
C04 A:U1H2601 4.2 33.2 0.7
CA A:GLY80 4.4 55.4 1.0
CZ A:PHE194 4.5 32.0 1.0
C12 A:U1H2601 4.5 39.6 0.7
CG2 A:ILE302 4.7 36.6 1.0
N A:GLY80 4.8 48.5 1.0
C03 A:U1H2601 4.9 37.5 0.7

Fluorine binding site 4 out of 6 in 7qmk

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Fluorine binding site 4 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:55.8
occ:0.68
 F08 A:U1H2606 0.0 55.8 0.7
C07 A:U1H2606 1.4 49.2 0.7
F10 A:U1H2606 2.2 52.9 0.7
F09 A:U1H2606 2.2 48.9 0.7
C06 A:U1H2606 2.3 40.6 0.7
C05 A:U1H2606 2.8 39.9 0.7
OD2 A:ASP119 3.4 57.1 1.0
C11 A:U1H2606 3.5 40.4 0.7
C1 A:DMS2603 4.0 27.5 0.6
C04 A:U1H2606 4.1 40.1 0.7
CD1 A:ILE122 4.3 26.0 1.0
CG A:ASP119 4.5 57.2 1.0
C12 A:U1H2606 4.6 39.3 0.7
C2 A:DMS2603 4.7 48.8 0.6
O A:HOH2709 4.7 21.7 1.0
C03 A:U1H2606 4.9 37.2 0.7
S A:DMS2603 4.9 38.5 0.6

Fluorine binding site 5 out of 6 in 7qmk

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Fluorine binding site 5 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:48.9
occ:0.68
 F09 A:U1H2606 0.0 48.9 0.7
C07 A:U1H2606 1.4 49.2 0.7
F10 A:U1H2606 2.2 52.9 0.7
F08 A:U1H2606 2.2 55.8 0.7
C06 A:U1H2606 2.4 40.6 0.7
C11 A:U1H2606 2.7 40.4 0.7
C05 A:U1H2606 3.6 39.9 0.7
OD2 A:ASP119 3.9 57.1 1.0
C12 A:U1H2606 4.1 39.3 0.7
CB A:SER115 4.1 41.4 1.0
OG A:SER115 4.1 40.6 1.0
OD2 A:ASP81 4.2 51.5 1.0
O A:SER115 4.3 33.0 1.0
CE1 A:PHE116 4.5 33.6 1.0
C2 A:DMS2603 4.6 48.8 0.6
C A:SER115 4.6 36.8 1.0
CD1 A:PHE116 4.7 30.1 1.0
C04 A:U1H2606 4.7 40.1 0.7
C03 A:U1H2606 4.9 37.2 0.7
CA A:SER115 5.0 35.6 1.0

Fluorine binding site 6 out of 6 in 7qmk

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Fluorine binding site 6 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 12) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:52.9
occ:0.68
 F10 A:U1H2606 0.0 52.9 0.7
C07 A:U1H2606 1.4 49.2 0.7
F08 A:U1H2606 2.2 55.8 0.7
F09 A:U1H2606 2.2 48.9 0.7
C06 A:U1H2606 2.4 40.6 0.7
C05 A:U1H2606 3.0 39.9 0.7
C11 A:U1H2606 3.4 40.4 0.7
CE1 A:PHE116 3.4 33.6 1.0
CD1 A:PHE116 3.5 30.1 1.0
OD2 A:ASP119 3.5 57.1 1.0
CD1 A:ILE122 4.1 26.0 1.0
C04 A:U1H2606 4.3 40.1 0.7
CG A:ASP119 4.3 57.2 1.0
CZ A:PHE116 4.4 33.7 1.0
O A:SER115 4.5 33.0 1.0
C12 A:U1H2606 4.5 39.3 0.7
CG A:PHE116 4.5 31.3 1.0
O A:HOH2791 4.5 29.0 1.0
CB A:ASP119 4.5 35.8 1.0
CA A:PHE116 4.8 30.6 1.0
C03 A:U1H2606 4.9 37.2 0.7
C A:SER115 4.9 36.8 1.0

Reference:

C.Y.Huang, S.Aumonier, S.Engilberge, D.Eris, K.M.L.Smith, F.Leonarski, J.A.Wojdyla, J.H.Beale, D.Buntschu, A.Pauluhn, M.E.Sharpe, A.Metz, V.Olieric, M.Wang. Probing Ligand Binding of Endothiapepsin By `Temperature-Resolved' Macromolecular Crystallography. Acta Crystallogr D Struct V. 78 964 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 35916221
DOI: 10.1107/S205979832200612X
Page generated: Fri Aug 2 11:35:46 2024

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