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Fluorine in PDB 5sli: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540, PDB code: 5sli was solved by N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 69.67 / 2.30
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 66.758, 69.462, 139.336, 90, 90, 90
R / Rfree (%) 20.8 / 27.1

Other elements in 5sli:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 also contains other interesting chemical elements:

Zinc (Zn) 3 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 (pdb code 5sli). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540, PDB code: 5sli:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 5sli

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Fluorine binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


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 NSP14 in Complex with Z1003146540 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F606

b:45.1
occ:1.00
 F1 D:LL0606 0.0 45.1 1.0
C7 D:LL0606 1.3 46.4 1.0
F2 D:LL0606 2.1 45.0 1.0
O3 D:LL0606 2.2 45.1 1.0
O2 D:LL0606 2.9 44.8 1.0
CD1 D:ILE474 3.1 39.3 1.0
CB D:THR516 3.3 42.1 1.0
NE1 D:TRP520 3.3 37.9 1.0
C6 D:LL0606 3.3 41.6 1.0
OG1 D:THR516 3.5 43.7 1.0
CG1 D:ILE474 3.6 40.0 1.0
C D:THR516 3.8 40.8 1.0
O D:THR516 3.8 46.5 1.0
CE2 D:TRP520 3.9 34.4 1.0
S1 D:LL0606 3.9 48.0 1.0
O D:ALA471 4.0 41.4 1.0
C1 D:LL0606 4.0 43.9 1.0
CZ2 D:TRP520 4.0 34.6 1.0
CA D:THR516 4.1 38.8 1.0
CD1 D:TRP520 4.2 38.4 1.0
N1 D:LL0606 4.2 42.9 1.0
C5 D:LL0606 4.3 42.3 1.0
N D:TYR517 4.3 37.6 1.0
CG2 D:THR516 4.4 43.6 1.0
CA D:TYR517 4.8 39.8 1.0
CD2 D:TRP520 5.0 34.5 1.0
CB D:ILE474 5.0 36.3 1.0

Fluorine binding site 2 out of 6 in 5sli

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Fluorine binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


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 NSP14 in Complex with Z1003146540 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F606

b:45.0
occ:1.00
 F2 D:LL0606 0.0 45.0 1.0
C7 D:LL0606 1.3 46.4 1.0
F1 D:LL0606 2.1 45.1 1.0
O3 D:LL0606 2.2 45.1 1.0
C6 D:LL0606 3.1 41.6 1.0
CD1 D:ILE474 3.4 39.3 1.0
C5 D:LL0606 3.4 42.3 1.0
O D:ALA471 3.4 41.4 1.0
CA D:THR472 3.6 41.0 1.0
CG1 D:ILE474 3.8 40.0 1.0
CB D:PHE445 3.8 37.2 1.0
CB D:THR516 3.8 42.1 1.0
OG1 D:THR516 4.0 43.7 1.0
CG2 D:THR472 4.1 36.8 1.0
O D:THR472 4.2 46.6 1.0
O D:HOH750 4.2 40.5 1.0
C D:ALA471 4.2 43.6 1.0
CG2 D:THR516 4.2 43.6 1.0
CB D:THR472 4.3 37.6 1.0
C D:THR472 4.3 43.1 1.0
C1 D:LL0606 4.3 43.9 1.0
N D:THR472 4.3 39.4 1.0
O2 D:LL0606 4.4 44.8 1.0
O D:PHE444 4.5 39.9 1.0
CA D:PHE445 4.6 36.9 1.0
C4 D:LL0606 4.7 45.2 1.0
CG D:PHE445 5.0 39.8 1.0
S1 D:LL0606 5.0 48.0 1.0

Fluorine binding site 3 out of 6 in 5sli

Go back to Fluorine Binding Sites List in 5sli
Fluorine binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F607

b:86.8
occ:1.00
 F1 D:LL0607 0.0 86.8 1.0
C7 D:LL0607 1.3 85.3 1.0
F2 D:LL0607 2.1 82.1 1.0
O3 D:LL0607 2.2 89.6 1.0
C6 D:LL0607 3.3 86.0 1.0
C5 D:LL0607 3.7 85.7 1.0
N1 D:LL0607 4.1 78.6 1.0
C1 D:LL0607 4.4 93.6 1.0
CB D:GLN513 4.5 43.9 1.0
OD1 D:ASP324 4.6 51.2 1.0
CG D:GLN513 4.6 47.5 1.0
O D:HOH973 4.8 40.8 1.0
S1 D:LL0607 4.9 71.7 1.0
O D:HOH832 4.9 56.7 1.0
CD D:GLN513 5.0 49.1 1.0

Fluorine binding site 4 out of 6 in 5sli

Go back to Fluorine Binding Sites List in 5sli
Fluorine binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F607

b:82.1
occ:1.00
 F2 D:LL0607 0.0 82.1 1.0
C7 D:LL0607 1.3 85.3 1.0
F1 D:LL0607 2.1 86.8 1.0
O3 D:LL0607 2.2 89.6 1.0
N1 D:LL0607 2.3 78.6 1.0
C6 D:LL0607 3.2 86.0 1.0
CB D:GLN513 3.5 43.9 1.0
S1 D:LL0607 3.5 71.7 1.0
C1 D:LL0607 3.7 93.6 1.0
CG D:GLN513 3.9 47.5 1.0
CD D:GLN513 4.0 49.1 1.0
OD1 D:ASP324 4.1 51.2 1.0
OE1 D:GLN513 4.2 54.4 1.0
O2 D:LL0607 4.2 70.3 1.0
CD2 D:TYR511 4.2 43.4 1.0
C5 D:LL0607 4.3 85.7 1.0
CE2 D:TYR511 4.3 41.6 1.0
O1 D:LL0607 4.5 54.5 1.0
CG D:ASP324 4.5 44.4 1.0
CE1 D:PHE326 4.5 34.1 1.0
CZ D:PHE326 4.6 33.7 1.0
NE2 D:GLN513 4.6 55.9 1.0
CB D:ASP324 4.7 41.4 1.0
CA D:GLN513 4.8 44.0 1.0
O D:HOH832 5.0 56.7 1.0

Fluorine binding site 5 out of 6 in 5sli

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Fluorine binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F608

b:84.6
occ:1.00
 F1 D:LL0608 0.0 84.6 1.0
C7 D:LL0608 1.3 73.3 1.0
F2 D:LL0608 2.1 72.4 1.0
O3 D:LL0608 2.2 77.6 1.0
C5 D:LL0608 2.3 71.9 1.0
C6 D:LL0608 2.6 74.0 1.0
C4 D:LL0608 3.6 81.9 1.0
C1 D:LL0608 4.0 77.2 1.0
C3 D:LL0608 4.7 80.5 1.0
O2 D:LL0608 4.8 60.5 1.0
C2 D:LL0608 4.8 81.5 1.0

Fluorine binding site 6 out of 6 in 5sli

Go back to Fluorine Binding Sites List in 5sli
Fluorine binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 NSP14 in Complex with Z1003146540 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F608

b:72.4
occ:1.00
 F2 D:LL0608 0.0 72.4 1.0
C7 D:LL0608 1.3 73.3 1.0
F1 D:LL0608 2.1 84.6 1.0
O3 D:LL0608 2.2 77.6 1.0
C6 D:LL0608 3.4 74.0 1.0
C5 D:LL0608 3.9 71.9 1.0
O2 D:LL0608 4.2 60.5 1.0
C1 D:LL0608 4.5 77.2 1.0
S1 D:LL0608 4.9 72.3 1.0

Reference:

N.Imprachim, Y.Yosaatmadja, F.Von-Delft, C.Bountra, O.Gileadi, J.A.Newman. Pandda Analysis Group Deposition To Be Published.
Page generated: Thu Aug 1 14:37:41 2024

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