Fluorine in PDB 7qmy: Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)

Enzymatic activity of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)

All present enzymatic activity of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8):
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8), PDB code: 7qmy 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) 37.37 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.981, 74.132, 53.529, 90, 109.78, 90
R / Rfree (%) 15.6 / 18.7

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8) (pdb code 7qmy). 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 Up Structure 8), PDB code: 7qmy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7qmy

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Fluorine binding site 1 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)


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 Up Structure 8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:59.3
occ:0.69
 F08 A:U1H2601 0.0 59.3 0.7
C07 A:U1H2601 1.4 60.8 0.7
F10 A:U1H2601 2.2 66.4 0.7
F09 A:U1H2601 2.3 58.2 0.7
C06 A:U1H2601 2.3 53.8 0.7
C05 A:U1H2601 2.6 51.2 0.7
CG2 A:ILE302 3.2 40.3 1.0
C11 A:U1H2601 3.6 56.5 0.7
CD1 A:ILE304 3.9 30.5 1.0
C04 A:U1H2601 4.0 42.6 0.7
CG2 A:ILE300 4.3 44.9 1.0
CG1 A:ILE304 4.5 25.1 1.0
CB A:ILE302 4.6 36.0 1.0
CD1 A:ILE217 4.6 30.0 1.0
CD1 A:ILE302 4.6 47.0 1.0
C12 A:U1H2601 4.7 52.7 0.7
CZ A:PHE194 4.8 34.6 1.0
C03 A:U1H2601 4.8 43.9 0.7

Fluorine binding site 2 out of 6 in 7qmy

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Fluorine binding site 2 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)


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 Up Structure 8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:58.2
occ:0.69
 F09 A:U1H2601 0.0 58.2 0.7
C07 A:U1H2601 1.4 60.8 0.7
F08 A:U1H2601 2.3 59.3 0.7
F10 A:U1H2601 2.3 66.4 0.7
C06 A:U1H2601 2.4 53.8 0.7
C11 A:U1H2601 2.8 56.5 0.7
CA A:GLY80 3.5 64.4 1.0
C05 A:U1H2601 3.6 51.2 0.7
CG2 A:ILE300 3.8 44.9 1.0
O A:DMS2604 4.1 63.7 0.7
C12 A:U1H2601 4.2 52.7 0.7
S A:DMS2604 4.2 61.4 0.7
CD1 A:ILE304 4.2 30.5 1.0
C A:GLY80 4.4 69.8 1.0
N A:GLY80 4.4 61.7 1.0
O A:GLY80 4.6 67.5 1.0
C1 A:DMS2604 4.6 48.9 0.7
C04 A:U1H2601 4.7 42.6 0.7
CG2 A:ILE302 4.7 40.3 1.0
C03 A:U1H2601 5.0 43.9 0.7

Fluorine binding site 3 out of 6 in 7qmy

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Fluorine binding site 3 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)


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 Up Structure 8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:66.4
occ:0.69
 F10 A:U1H2601 0.0 66.4 0.7
C07 A:U1H2601 1.4 60.8 0.7
F08 A:U1H2601 2.2 59.3 0.7
F09 A:U1H2601 2.3 58.2 0.7
C06 A:U1H2601 2.3 53.8 0.7
C05 A:U1H2601 3.1 51.2 0.7
C11 A:U1H2601 3.2 56.5 0.7
CA A:GLY80 4.2 64.4 1.0
C04 A:U1H2601 4.3 42.6 0.7
C12 A:U1H2601 4.4 52.7 0.7
C2 A:DMS2605 4.5 54.5 0.7
N A:GLY80 4.7 61.7 1.0
CZ A:PHE194 4.8 34.6 1.0
C03 A:U1H2601 4.9 43.9 0.7
CG2 A:ILE302 4.9 40.3 1.0
C1 A:DMS2605 5.0 58.2 0.7

Fluorine binding site 4 out of 6 in 7qmy

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Fluorine binding site 4 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)


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 Up Structure 8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:60.0
occ:0.70
 F08 A:U1H2606 0.0 60.0 0.7
C07 A:U1H2606 1.4 56.1 0.7
F09 A:U1H2606 2.2 55.4 0.7
F10 A:U1H2606 2.3 56.4 0.7
C06 A:U1H2606 2.4 47.8 0.7
C05 A:U1H2606 3.1 44.5 0.7
OD2 A:ASP119 3.3 64.2 1.0
C11 A:U1H2606 3.4 50.4 0.7
C1 A:DMS2603 3.8 38.9 0.6
C2 A:DMS2603 4.2 50.8 0.6
C04 A:U1H2606 4.3 43.5 0.7
CG A:ASP119 4.5 63.7 1.0
C12 A:U1H2606 4.5 47.2 0.7
S A:DMS2603 4.6 43.6 0.6
C03 A:U1H2606 4.9 44.1 0.7
CD1 A:ILE122 5.0 32.4 1.0

Fluorine binding site 5 out of 6 in 7qmy

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Fluorine binding site 5 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)


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 Up Structure 8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:55.4
occ:0.70
 F09 A:U1H2606 0.0 55.4 0.7
C07 A:U1H2606 1.4 56.1 0.7
F08 A:U1H2606 2.2 60.0 0.7
F10 A:U1H2606 2.3 56.4 0.7
C06 A:U1H2606 2.4 47.8 0.7
C11 A:U1H2606 2.7 50.4 0.7
OG A:SER115 3.5 51.4 1.0
C05 A:U1H2606 3.6 44.5 0.7
OG A:SER83 3.7 61.4 1.0
CB A:SER115 3.8 51.0 1.0
OD2 A:ASP119 3.9 64.2 1.0
CE1 A:PHE116 4.0 45.6 1.0
OD2 A:ASP81 4.1 65.8 1.0
C12 A:U1H2606 4.1 47.2 0.7
O A:SER115 4.1 46.1 1.0
C A:SER115 4.2 47.3 1.0
CD1 A:PHE116 4.2 41.6 1.0
CZ A:PHE116 4.5 44.9 1.0
N A:PHE116 4.5 43.2 1.0
CA A:SER115 4.6 47.6 1.0
CB A:SER83 4.8 55.8 1.0
C04 A:U1H2606 4.8 43.5 0.7
CG A:PHE116 4.8 40.4 1.0
C2 A:DMS2603 4.9 50.8 0.6
CA A:PHE116 5.0 43.0 1.0
C03 A:U1H2606 5.0 44.1 0.7

Fluorine binding site 6 out of 6 in 7qmy

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Fluorine binding site 6 out of 6 in the Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Up Structure 8)


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 Up Structure 8) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:56.4
occ:0.70
 F10 A:U1H2606 0.0 56.4 0.7
C07 A:U1H2606 1.4 56.1 0.7
F08 A:U1H2606 2.3 60.0 0.7
F09 A:U1H2606 2.3 55.4 0.7
C06 A:U1H2606 2.4 47.8 0.7
C05 A:U1H2606 2.8 44.5 0.7
OD2 A:ASP119 3.3 64.2 1.0
C11 A:U1H2606 3.5 50.4 0.7
CE1 A:PHE116 3.6 45.6 1.0
CD1 A:PHE116 3.7 41.6 1.0
CD1 A:ILE122 3.9 32.4 1.0
C04 A:U1H2606 4.1 43.5 0.7
CG A:ASP119 4.2 63.7 1.0
CB A:ASP119 4.5 49.0 1.0
O A:SER115 4.6 46.1 1.0
O A:HOH2793 4.6 37.4 1.0
C12 A:U1H2606 4.7 47.2 0.7
CZ A:PHE116 4.7 44.9 1.0
CG A:PHE116 4.7 40.4 1.0
C03 A:U1H2606 4.9 44.1 0.7
CA A:PHE116 4.9 43.0 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: Wed Apr 5 00:48:17 2023

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