Fluorine in PDB 8gia: Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr

Enzymatic activity of Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr

All present enzymatic activity of Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr:
3.4.19.121;

Protein crystallography data

The structure of Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr, PDB code: 8gia was solved by S.D.Wallace, S.R.Bagde, J.C.Fromme, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 68.92 / 1.86
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 140.517, 36.668, 65.056, 90, 101.21, 90
R / Rfree (%) 20.8 / 25.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr (pdb code 8gia). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr, PDB code: 8gia:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 8gia

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Fluorine binding site 1 out of 6 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:45.1
occ:1.00
 F29 C:ZJ3201 0.0 45.1 1.0
C28 C:ZJ3201 1.3 42.2 1.0
F31 C:ZJ3201 2.2 49.6 1.0
F30 C:ZJ3201 2.2 52.7 1.0
C27 C:ZJ3201 2.4 37.3 1.0
H251 C:ZJ3201 2.4 36.2 1.0
C26 C:ZJ3201 3.0 35.0 1.0
C25 C:ZJ3201 3.0 30.1 1.0
C32 C:ZJ3201 3.4 43.9 1.0
H321 C:ZJ3201 3.7 52.7 1.0
C36 C:ZJ3201 4.3 32.2 1.0
C24 C:ZJ3201 4.3 31.5 1.0
C33 C:ZJ3201 4.6 42.6 1.0
CD1 C:ILE131 4.7 47.8 1.0
H241 C:ZJ3201 4.8 37.9 1.0
O34 C:ZJ3201 4.9 36.2 1.0

Fluorine binding site 2 out of 6 in 8gia

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Fluorine binding site 2 out of 6 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:52.7
occ:1.00
 F30 C:ZJ3201 0.0 52.7 1.0
C28 C:ZJ3201 1.3 42.2 1.0
F29 C:ZJ3201 2.2 45.1 1.0
F31 C:ZJ3201 2.2 49.6 1.0
H251 C:ZJ3201 2.4 36.2 1.0
C27 C:ZJ3201 2.4 37.3 1.0
C25 C:ZJ3201 3.0 30.1 1.0
C26 C:ZJ3201 3.0 35.0 1.0
C32 C:ZJ3201 3.5 43.9 1.0
H321 C:ZJ3201 3.8 52.7 1.0
C24 C:ZJ3201 4.3 31.5 1.0
O C:GLY46 4.3 28.4 1.0
C36 C:ZJ3201 4.3 32.2 1.0
C33 C:ZJ3201 4.7 42.6 1.0
H241 C:ZJ3201 4.7 37.9 1.0
O34 C:ZJ3201 4.9 36.2 1.0

Fluorine binding site 3 out of 6 in 8gia

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Fluorine binding site 3 out of 6 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F201

b:49.6
occ:1.00
 F31 C:ZJ3201 0.0 49.6 1.0
C28 C:ZJ3201 1.3 42.2 1.0
F29 C:ZJ3201 2.2 45.1 1.0
F30 C:ZJ3201 2.2 52.7 1.0
C27 C:ZJ3201 2.4 37.3 1.0
H321 C:ZJ3201 2.4 52.7 1.0
C32 C:ZJ3201 2.7 43.9 1.0
C26 C:ZJ3201 3.7 35.0 1.0
H251 C:ZJ3201 3.9 36.2 1.0
C33 C:ZJ3201 4.1 42.6 1.0
C25 C:ZJ3201 4.3 30.1 1.0
C36 C:ZJ3201 4.8 32.2 1.0
O35 C:ZJ3201 4.8 52.6 1.0
O34 C:ZJ3201 4.9 36.2 1.0

Fluorine binding site 4 out of 6 in 8gia

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Fluorine binding site 4 out of 6 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:43.7
occ:1.00
 F29 A:ZJ3201 0.0 43.7 1.0
C28 A:ZJ3201 1.3 40.0 1.0
F31 A:ZJ3201 2.2 46.3 1.0
F30 A:ZJ3201 2.2 51.0 1.0
C27 A:ZJ3201 2.3 44.5 1.0
H251 A:ZJ3201 2.4 42.3 1.0
C25 A:ZJ3201 3.0 35.3 1.0
C26 A:ZJ3201 3.0 38.5 1.0
C32 A:ZJ3201 3.4 45.5 1.0
H321 A:ZJ3201 3.7 54.6 1.0
C24 A:ZJ3201 4.3 30.3 1.0
CD1 A:ILE131 4.3 43.5 1.0
C36 A:ZJ3201 4.3 31.7 1.0
C33 A:ZJ3201 4.6 43.9 1.0
CG1 A:ILE131 4.7 36.0 1.0
H241 A:ZJ3201 4.7 36.3 1.0
O34 A:ZJ3201 4.9 41.2 1.0
O A:HOH323 4.9 35.6 1.0

Fluorine binding site 5 out of 6 in 8gia

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Fluorine binding site 5 out of 6 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:51.0
occ:1.00
 F30 A:ZJ3201 0.0 51.0 1.0
C28 A:ZJ3201 1.3 40.0 1.0
F29 A:ZJ3201 2.2 43.7 1.0
F31 A:ZJ3201 2.2 46.3 1.0
C27 A:ZJ3201 2.4 44.5 1.0
H251 A:ZJ3201 2.4 42.3 1.0
O A:HOH323 2.9 35.6 1.0
C25 A:ZJ3201 3.0 35.3 1.0
C26 A:ZJ3201 3.0 38.5 1.0
C32 A:ZJ3201 3.5 45.5 1.0
H321 A:ZJ3201 3.7 54.6 1.0
C24 A:ZJ3201 4.3 30.3 1.0
C36 A:ZJ3201 4.3 31.7 1.0
O A:GLY46 4.6 28.2 1.0
C33 A:ZJ3201 4.6 43.9 1.0
H241 A:ZJ3201 4.8 36.3 1.0
O34 A:ZJ3201 4.9 41.2 1.0

Fluorine binding site 6 out of 6 in 8gia

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Fluorine binding site 6 out of 6 in the Crystal Structure of Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr


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 Sars-Cov-2 (Covid-19) NSP3 Macrodomain in Complex with Tfmu-Adpr within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:46.3
occ:1.00
 F31 A:ZJ3201 0.0 46.3 1.0
C28 A:ZJ3201 1.3 40.0 1.0
F29 A:ZJ3201 2.2 43.7 1.0
F30 A:ZJ3201 2.2 51.0 1.0
C27 A:ZJ3201 2.4 44.5 1.0
H321 A:ZJ3201 2.4 54.6 1.0
C32 A:ZJ3201 2.7 45.5 1.0
C26 A:ZJ3201 3.7 38.5 1.0
H251 A:ZJ3201 3.9 42.3 1.0
C33 A:ZJ3201 4.1 43.9 1.0
C25 A:ZJ3201 4.3 35.3 1.0
O A:HOH323 4.5 35.6 1.0
C36 A:ZJ3201 4.8 31.7 1.0
O35 A:ZJ3201 4.9 56.9 1.0
O34 A:ZJ3201 4.9 41.2 1.0

Reference:

A.Anmangandla, S.Jana, K.Peng, S.D.Wallace, S.R.Bagde, B.S.Drown, J.Xu, P.J.Hergenrother, J.C.Fromme, H.Lin. A Fluorescence Polarization Assay For Macrodomains Facilitates the Identification of Potent Inhibitors of the Sars-Cov-2 Macrodomain. Acs Chem.Biol. 2023.
ISSN: ESSN 1554-8937
PubMed: 37126856
DOI: 10.1021/ACSCHEMBIO.3C00092
Page generated: Fri Aug 2 19:47:26 2024

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