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

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

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

Protein crystallography data

The structure of Endothiapepsin in Complex with Compound TL00150 at Room-Temperature (Temperature Ramping Down Structure 8), PDB code: 7qmg 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) 35.25 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.884, 74.017, 53.402, 90, 109.52, 90
R / Rfree (%) 18.6 / 22.3

Fluorine Binding Sites:

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

Fluorine binding site 1 out of 6 in 7qmg

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

b:53.6
occ:0.67
 F08 A:U1H2601 0.0 53.6 0.7
C07 A:U1H2601 1.4 54.0 0.7
F10 A:U1H2601 2.2 56.0 0.7
F09 A:U1H2601 2.2 54.1 0.7
C06 A:U1H2601 2.3 47.9 0.7
C05 A:U1H2601 2.8 44.8 0.7
CG2 A:ILE302 3.1 41.1 1.0
C11 A:U1H2601 3.5 49.1 0.7
CD1 A:ILE304 3.6 34.7 1.0
C04 A:U1H2601 4.1 39.7 0.7
CG2 A:ILE300 4.2 42.7 1.0
CG1 A:ILE304 4.2 29.1 1.0
C1 A:DMS2604 4.5 54.5 0.6
CD1 A:ILE217 4.6 30.7 1.0
CB A:ILE302 4.6 35.7 1.0
C12 A:U1H2601 4.6 44.5 0.7
C03 A:U1H2601 4.9 39.5 0.7

Fluorine binding site 2 out of 6 in 7qmg

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

b:54.1
occ:0.67
 F09 A:U1H2601 0.0 54.1 0.7
C07 A:U1H2601 1.4 54.0 0.7
F08 A:U1H2601 2.2 53.6 0.7
F10 A:U1H2601 2.2 56.0 0.7
C06 A:U1H2601 2.4 47.9 0.7
C11 A:U1H2601 2.7 49.1 0.7
C1 A:DMS2604 3.2 54.5 0.6
CA A:GLY80 3.4 62.4 1.0
C05 A:U1H2601 3.6 44.8 0.7
CG2 A:ILE300 3.8 42.7 1.0
C12 A:U1H2601 4.1 44.5 0.7
N A:GLY80 4.2 61.6 1.0
C A:GLY80 4.3 63.6 1.0
CD1 A:ILE304 4.4 34.7 1.0
O A:GLY80 4.5 64.8 1.0
S A:DMS2604 4.7 60.1 0.6
CG2 A:ILE302 4.7 41.1 1.0
C04 A:U1H2601 4.8 39.7 0.7
C03 A:U1H2601 5.0 39.5 0.7

Fluorine binding site 3 out of 6 in 7qmg

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

b:56.0
occ:0.67
 F10 A:U1H2601 0.0 56.0 0.7
C07 A:U1H2601 1.4 54.0 0.7
F08 A:U1H2601 2.2 53.6 0.7
F09 A:U1H2601 2.2 54.1 0.7
C06 A:U1H2601 2.3 47.9 0.7
C05 A:U1H2601 2.9 44.8 0.7
C11 A:U1H2601 3.4 49.1 0.7
C1 A:DMS2605 4.1 48.3 0.6
C04 A:U1H2601 4.2 39.7 0.7
CZ A:PHE194 4.5 36.0 1.0
CA A:GLY80 4.5 62.4 1.0
C12 A:U1H2601 4.5 44.5 0.7
CG2 A:ILE302 4.6 41.1 1.0
N A:GLY80 4.8 61.6 1.0
C03 A:U1H2601 4.8 39.5 0.7

Fluorine binding site 4 out of 6 in 7qmg

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

b:53.6
occ:0.63
 F08 A:U1H2606 0.0 53.6 0.6
C07 A:U1H2606 1.4 52.2 0.6
F10 A:U1H2606 2.2 53.7 0.6
F09 A:U1H2606 2.2 53.1 0.6
C06 A:U1H2606 2.3 48.3 0.6
C05 A:U1H2606 2.8 44.9 0.6
OD2 A:ASP119 3.2 56.4 1.0
C11 A:U1H2606 3.5 49.9 0.6
C04 A:U1H2606 4.1 42.8 0.6
C1 A:DMS2603 4.2 35.3 0.5
O A:HOH2741 4.3 52.9 1.0
C2 A:DMS2603 4.3 47.3 0.5
CG A:ASP119 4.4 55.2 1.0
CD1 A:ILE122 4.7 34.9 1.0
C12 A:U1H2606 4.7 49.6 0.6
S A:DMS2603 4.9 39.4 0.5
C03 A:U1H2606 4.9 44.3 0.6
O A:HOH2704 5.0 28.1 1.0

Fluorine binding site 5 out of 6 in 7qmg

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

b:53.1
occ:0.63
 F09 A:U1H2606 0.0 53.1 0.6
C07 A:U1H2606 1.4 52.2 0.6
F10 A:U1H2606 2.2 53.7 0.6
F08 A:U1H2606 2.2 53.6 0.6
C06 A:U1H2606 2.3 48.3 0.6
C11 A:U1H2606 2.7 49.9 0.6
OG A:SER115 3.5 52.6 1.0
C05 A:U1H2606 3.6 44.9 0.6
OD2 A:ASP81 3.7 61.7 1.0
OG A:SER83 3.8 60.7 1.0
CB A:SER115 3.9 54.9 1.0
C12 A:U1H2606 4.0 49.6 0.6
OD2 A:ASP119 4.1 56.4 1.0
C2 A:DMS2603 4.2 47.3 0.5
O A:SER115 4.3 47.5 1.0
C A:SER115 4.6 49.5 1.0
C04 A:U1H2606 4.7 42.8 0.6
CE1 A:PHE116 4.7 44.0 1.0
CG A:ASP81 4.8 63.9 1.0
CB A:SER83 4.8 54.6 1.0
CA A:SER115 4.9 53.9 1.0
C03 A:U1H2606 4.9 44.3 0.6
CD1 A:PHE116 4.9 43.0 1.0

Fluorine binding site 6 out of 6 in 7qmg

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

b:53.7
occ:0.63
 F10 A:U1H2606 0.0 53.7 0.6
C07 A:U1H2606 1.4 52.2 0.6
F08 A:U1H2606 2.2 53.6 0.6
F09 A:U1H2606 2.2 53.1 0.6
C06 A:U1H2606 2.4 48.3 0.6
C05 A:U1H2606 3.1 44.9 0.6
C11 A:U1H2606 3.3 49.9 0.6
OD2 A:ASP119 3.3 56.4 1.0
CD1 A:PHE116 3.4 43.0 1.0
CE1 A:PHE116 3.4 44.0 1.0
O A:SER115 4.0 47.5 1.0
CG A:PHE116 4.3 45.6 1.0
CZ A:PHE116 4.3 46.7 1.0
CG A:ASP119 4.3 55.2 1.0
C04 A:U1H2606 4.4 42.8 0.6
C A:SER115 4.5 49.5 1.0
CA A:PHE116 4.5 46.0 1.0
OG A:SER115 4.5 52.6 1.0
C12 A:U1H2606 4.5 49.6 0.6
CB A:ASP119 4.6 46.2 1.0
N A:PHE116 4.7 46.3 1.0
CD1 A:ILE122 4.7 34.9 1.0
O A:HOH2796 4.7 37.8 1.0
C03 A:U1H2606 4.9 44.3 0.6
CB A:PHE116 5.0 44.4 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 11:35:18 2024

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