Fluorine in PDB 7qm6: Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K

Enzymatic activity of Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K

All present enzymatic activity of Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K:
3.4.23.22;

Protein crystallography data

The structure of Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K, PDB code: 7qm6 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 / 1.81
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 45.981, 74.092, 53.454, 90, 109.72, 90
R / Rfree (%) 15.2 / 18.5

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K (pdb code 7qm6). 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 in 15% Dmso at 298 K, PDB code: 7qm6:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7qm6

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Fluorine binding site 1 out of 6 in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K


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 in 15% Dmso at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:65.8
occ:0.77
 F08 A:U1H2601 0.0 65.8 0.8
C07 A:U1H2601 1.4 65.5 0.8
F10 A:U1H2601 2.2 66.9 0.8
F09 A:U1H2601 2.2 56.1 0.8
C06 A:U1H2601 2.4 54.1 0.8
C05 A:U1H2601 2.8 58.1 0.8
CG2 A:ILE302 3.1 40.8 1.0
C11 A:U1H2601 3.6 58.0 0.8
CD1 A:ILE304 3.8 31.9 1.0
C04 A:U1H2601 4.1 46.0 0.8
CG2 A:ILE300 4.3 49.3 1.0
CG1 A:ILE304 4.4 25.3 1.0
CB A:ILE302 4.5 30.0 1.0
CD1 A:ILE217 4.6 28.6 1.0
C12 A:U1H2601 4.7 55.6 0.8
CD1 A:ILE302 4.8 52.9 1.0
CZ A:PHE194 4.9 35.0 1.0
C03 A:U1H2601 4.9 46.5 0.8

Fluorine binding site 2 out of 6 in 7qm6

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Fluorine binding site 2 out of 6 in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K


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 in 15% Dmso at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:56.1
occ:0.77
 F09 A:U1H2601 0.0 56.1 0.8
C07 A:U1H2601 1.4 65.5 0.8
F10 A:U1H2601 2.2 66.9 0.8
F08 A:U1H2601 2.2 65.8 0.8
C06 A:U1H2601 2.4 54.1 0.8
C11 A:U1H2601 2.7 58.0 0.8
CA A:GLY80 3.5 75.5 1.0
C05 A:U1H2601 3.6 58.1 0.8
CG2 A:ILE300 3.9 49.3 1.0
O A:DMS2604 3.9 79.0 0.8
C12 A:U1H2601 4.1 55.6 0.8
CD1 A:ILE304 4.1 31.9 1.0
S A:DMS2604 4.3 70.5 0.8
N A:GLY80 4.4 69.7 1.0
C A:GLY80 4.4 86.4 1.0
C1 A:DMS2604 4.5 60.9 0.8
O A:GLY80 4.5 74.5 1.0
C04 A:U1H2601 4.7 46.0 0.8
CG2 A:ILE302 4.8 40.8 1.0
C03 A:U1H2601 4.9 46.5 0.8

Fluorine binding site 3 out of 6 in 7qm6

Go back to Fluorine Binding Sites List in 7qm6
Fluorine binding site 3 out of 6 in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K


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 in 15% Dmso at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2601

b:66.9
occ:0.77
 F10 A:U1H2601 0.0 66.9 0.8
C07 A:U1H2601 1.4 65.5 0.8
F08 A:U1H2601 2.2 65.8 0.8
F09 A:U1H2601 2.2 56.1 0.8
C06 A:U1H2601 2.4 54.1 0.8
C05 A:U1H2601 3.2 58.1 0.8
C11 A:U1H2601 3.2 58.0 0.8
CA A:GLY80 4.2 75.5 1.0
C04 A:U1H2601 4.4 46.0 0.8
C12 A:U1H2601 4.4 55.6 0.8
C1 A:DMS2605 4.6 72.0 0.9
N A:GLY80 4.7 69.7 1.0
CZ A:PHE194 4.8 35.0 1.0
C03 A:U1H2601 4.9 46.5 0.8
CG2 A:ILE302 4.9 40.8 1.0

Fluorine binding site 4 out of 6 in 7qm6

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Fluorine binding site 4 out of 6 in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K


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 in 15% Dmso at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:69.0
occ:0.76
 F08 A:U1H2606 0.0 69.0 0.8
C07 A:U1H2606 1.4 65.4 0.8
F10 A:U1H2606 2.2 63.5 0.8
F09 A:U1H2606 2.2 68.5 0.8
C06 A:U1H2606 2.4 52.5 0.8
C05 A:U1H2606 3.0 50.2 0.8
C11 A:U1H2606 3.4 60.5 0.8
OD2 A:ASP119 3.7 68.7 1.0
C1 A:DMS2603 3.9 42.7 0.6
C04 A:U1H2606 4.2 49.2 0.8
C2 A:DMS2603 4.3 58.0 0.6
C12 A:U1H2606 4.6 55.6 0.8
S A:DMS2603 4.6 46.3 0.6
CG A:ASP119 4.9 70.2 1.0
C03 A:U1H2606 4.9 48.6 0.8
CD1 A:ILE122 4.9 36.4 1.0

Fluorine binding site 5 out of 6 in 7qm6

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Fluorine binding site 5 out of 6 in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K


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 in 15% Dmso at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:68.5
occ:0.76
 F09 A:U1H2606 0.0 68.5 0.8
C07 A:U1H2606 1.4 65.4 0.8
F08 A:U1H2606 2.2 69.0 0.8
F10 A:U1H2606 2.2 63.5 0.8
C06 A:U1H2606 2.4 52.5 0.8
C11 A:U1H2606 2.7 60.5 0.8
OG A:SER115 3.5 59.0 1.0
C05 A:U1H2606 3.6 50.2 0.8
OG A:SER83 3.8 77.4 1.0
CB A:SER115 3.8 49.8 1.0
CE1 A:PHE116 4.0 42.1 1.0
O A:SER115 4.0 48.1 1.0
C12 A:U1H2606 4.1 55.6 0.8
OD2 A:ASP81 4.1 76.4 1.0
CD1 A:PHE116 4.2 40.3 1.0
C A:SER115 4.2 50.6 1.0
CZ A:PHE116 4.5 44.7 1.0
OD2 A:ASP119 4.6 68.7 1.0
N A:PHE116 4.6 43.1 1.0
CA A:SER115 4.7 47.9 1.0
C04 A:U1H2606 4.8 49.2 0.8
CG A:PHE116 4.8 42.0 1.0
CB A:SER83 4.8 62.9 1.0
C03 A:U1H2606 4.9 48.6 0.8
CA A:PHE116 5.0 38.4 1.0
C2 A:DMS2603 5.0 58.0 0.6

Fluorine binding site 6 out of 6 in 7qm6

Go back to Fluorine Binding Sites List in 7qm6
Fluorine binding site 6 out of 6 in the Endothiapepsin in Complex with Compound TL00150 in 15% Dmso at 298 K


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 in 15% Dmso at 298 K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F2606

b:63.5
occ:0.76
 F10 A:U1H2606 0.0 63.5 0.8
C07 A:U1H2606 1.4 65.4 0.8
F08 A:U1H2606 2.2 69.0 0.8
F09 A:U1H2606 2.2 68.5 0.8
C06 A:U1H2606 2.3 52.5 0.8
C05 A:U1H2606 2.9 50.2 0.8
C11 A:U1H2606 3.5 60.5 0.8
OD2 A:ASP119 3.5 68.7 1.0
CE1 A:PHE116 3.6 42.1 1.0
CD1 A:PHE116 3.6 40.3 1.0
CD1 A:ILE122 4.0 36.4 1.0
C04 A:U1H2606 4.2 49.2 0.8
CG A:ASP119 4.4 70.2 1.0
O A:SER115 4.5 48.1 1.0
CB A:ASP119 4.5 47.7 1.0
C12 A:U1H2606 4.6 55.6 0.8
CZ A:PHE116 4.6 44.7 1.0
CG A:PHE116 4.7 42.0 1.0
O A:HOH2799 4.8 39.9 1.0
CA A:PHE116 4.9 38.4 1.0
C03 A:U1H2606 4.9 48.6 0.8

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 11:31:56 2024

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