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Fluorine in PDB 5sr4: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers:
3.4.19.121;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers, PDB code: 5sr4 was solved by G.J.Correy, J.S.Fraser, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.72 / 1.05
Space group P 43
Cell size a, b, c (Å), α, β, γ (°) 88.818, 88.818, 39.54, 90, 90, 90
R / Rfree (%) 14 / 15.6

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers (pdb code 5sr4). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers, PDB code: 5sr4:
Jump to Fluorine binding site number: 1; 2;

Fluorine binding site 1 out of 2 in 5sr4

Go back to Fluorine Binding Sites List in 5sr4
Fluorine binding site 1 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F201

b:15.4
occ:0.07
 F15 A:QYO201 0.0 15.4 0.1
F15 A:QYU202 0.3 15.3 0.1
C12 A:QYU202 1.2 15.1 0.1
O A:HOH442 1.2 14.9 0.9
C12 A:QYO201 1.3 15.3 0.1
O A:HOH537 1.5 39.3 0.9
C13 A:QYU202 2.3 15.1 0.1
C11 A:QYU202 2.3 15.0 0.1
C13 A:QYO201 2.4 15.3 0.1
C11 A:QYO201 2.4 15.3 0.1
HB2 A:ALA52 2.5 14.8 1.0
H131 A:QYO201 2.5 18.4 0.1
H111 A:QYO201 2.5 18.4 0.1
H131 A:QYU202 2.6 18.1 0.1
H111 A:QYU202 2.6 18.0 0.1
O A:HOH538 3.3 59.1 1.0
CB A:ALA52 3.4 12.3 1.0
O A:HOH530 3.4 32.5 0.9
C14 A:QYU202 3.5 15.1 0.1
C10 A:QYU202 3.6 15.0 0.1
HB1 A:ALA52 3.6 14.8 1.0
C14 A:QYO201 3.6 15.3 0.1
C10 A:QYO201 3.6 15.4 0.1
HB3 A:ALA52 3.7 14.8 1.0
O A:GLY48 3.8 14.5 0.1
O A:GLY48 3.9 11.7 0.9
C09 A:QYU202 4.1 15.1 0.1
C09 A:QYO201 4.2 15.5 0.1
H141 A:QYU202 4.4 18.1 0.1
H A:ALA52 4.4 12.3 1.0
C A:GLY48 4.4 14.1 0.1
HA A:ALA52 4.4 12.8 1.0
HA2 A:GLY48 4.4 16.9 0.1
CA A:ALA52 4.4 10.7 1.0
H141 A:QYO201 4.5 18.4 0.1
HE2 A:PHE156 4.5 23.5 0.1
C A:GLY48 4.6 11.2 0.9
H A:GLY48 4.7 16.7 0.1
N A:ALA52 4.7 10.2 1.0
HA2 A:GLY48 4.8 14.8 0.9
CA A:GLY48 4.8 14.1 0.1
N16 A:QYU202 4.9 14.9 0.1
N16 A:QYO201 4.9 15.4 0.1
N A:GLY48 5.0 13.9 0.1

Fluorine binding site 2 out of 2 in 5sr4

Go back to Fluorine Binding Sites List in 5sr4
Fluorine binding site 2 out of 2 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP3 Macrodomain in Complex with Z2479779298 - (R,S) and (S,R) Isomers within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F202

b:15.3
occ:0.07
 F15 A:QYU202 0.0 15.3 0.1
F15 A:QYO201 0.3 15.4 0.1
C12 A:QYU202 0.9 15.1 0.1
C12 A:QYO201 1.0 15.3 0.1
O A:HOH442 1.1 14.9 0.9
O A:HOH537 1.7 39.3 0.9
C13 A:QYU202 2.0 15.1 0.1
C11 A:QYU202 2.0 15.0 0.1
C13 A:QYO201 2.1 15.3 0.1
C11 A:QYO201 2.1 15.3 0.1
H111 A:QYO201 2.4 18.4 0.1
H131 A:QYO201 2.4 18.4 0.1
H111 A:QYU202 2.4 18.0 0.1
H131 A:QYU202 2.4 18.1 0.1
HB2 A:ALA52 2.5 14.8 1.0
O A:HOH530 3.2 32.5 0.9
C14 A:QYU202 3.2 15.1 0.1
C10 A:QYU202 3.3 15.0 0.1
CB A:ALA52 3.3 12.3 1.0
C10 A:QYO201 3.4 15.4 0.1
C14 A:QYO201 3.4 15.3 0.1
HB1 A:ALA52 3.5 14.8 1.0
O A:HOH538 3.5 59.1 1.0
HB3 A:ALA52 3.6 14.8 1.0
O A:GLY48 3.7 14.5 0.1
O A:GLY48 3.8 11.7 0.9
C09 A:QYU202 3.8 15.1 0.1
C09 A:QYO201 3.9 15.5 0.1
H141 A:QYU202 4.1 18.1 0.1
H141 A:QYO201 4.2 18.4 0.1
C A:GLY48 4.3 14.1 0.1
HA2 A:GLY48 4.3 16.9 0.1
H A:ALA52 4.4 12.3 1.0
HE2 A:PHE156 4.4 23.5 0.1
CA A:ALA52 4.5 10.7 1.0
C A:GLY48 4.5 11.2 0.9
HA A:ALA52 4.5 12.8 1.0
N16 A:QYU202 4.6 14.9 0.1
N16 A:QYO201 4.6 15.4 0.1
HA2 A:GLY48 4.7 14.8 0.9
H A:GLY48 4.7 16.7 0.1
N A:ALA52 4.7 10.2 1.0
CA A:GLY48 4.7 14.1 0.1
HA A:VAL49 4.8 12.7 0.9
HA A:VAL49 4.8 15.6 0.1
CE2 A:PHE156 4.9 19.6 0.1
N A:GLY48 5.0 13.9 0.1
H161 A:QYO201 5.0 18.5 0.1

Reference:

S.Gahbauer, G.J.Correy, M.Schuller, M.P.Ferla, Y.U.Doruk, M.Rachman, T.Wu, M.Diolaiti, S.Wang, R.J.Neitz, D.Fearon, D.Radchenko, Y.Moroz, J.J.Irwin, A.R.Renslo, J.C.Taylor, J.E.Gestwicki, F.Von Delft, A.Ashworth, I.Ahel, B.K.Shoichet, J.S.Fraser. Structure-Based Inhibitor Optimization For the NSP3 Macrodomain of Sars-Cov-2. Biorxiv 2022.
ISSN: ISSN 2692-8205
PubMed: 35794891
DOI: 10.1101/2022.06.27.497816
Page generated: Thu Aug 1 14:47:29 2024

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