Zinc in PDB 5rl7: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922:
3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922, PDB code: 5rl7 was solved by J.A.Newman, Y.Yosaatmadja, A.Douangamath, A.Aimon, A.J.Powell, A.Dias, D.Fearon, L.Dunnett, J.Brandao-Neto, T.Krojer, R.Skyner, T.Gorrie-Stone, W.Thompson, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 81.45 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.145, 70.281, 85.587, 102.73, 96.54, 112.33
R / Rfree (%) 22.7 / 26.9

Other elements in 5rl7:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 (pdb code 5rl7). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 6 binding sites of Zinc where determined in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922, PDB code: 5rl7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rl7

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Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:36.2
occ:1.00
 NE2 B:HIS33 2.1 34.6 1.0
SG B:CYS16 2.1 40.6 1.0
ND1 B:HIS39 2.2 40.6 1.0
SG B:CYS19 2.4 42.0 1.0
CD2 B:HIS33 3.0 32.1 1.0
CG B:HIS39 3.1 42.8 1.0
CE1 B:HIS33 3.2 39.3 1.0
CB B:CYS16 3.2 43.0 1.0
CE1 B:HIS39 3.2 44.3 1.0
CB B:HIS39 3.3 39.9 1.0
CB B:CYS19 3.4 39.2 1.0
N B:CYS19 3.4 44.4 1.0
CA B:CYS19 3.7 41.2 1.0
CG B:HIS33 4.2 33.8 1.0
ND1 B:HIS33 4.2 34.6 1.0
CD2 B:HIS39 4.3 45.1 1.0
C B:ALA18 4.3 43.5 1.0
NE2 B:HIS39 4.3 46.1 1.0
CA B:CYS16 4.6 43.5 1.0
CB B:ALA18 4.6 40.6 1.0
CB B:ALA110 4.7 36.5 1.0
CA B:HIS39 4.8 40.1 1.0
CA B:ALA18 4.8 42.5 1.0
N B:ALA18 4.8 45.3 1.0
C B:CYS16 4.9 45.1 1.0

Zinc binding site 2 out of 6 in 5rl7

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Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:53.0
occ:1.00
 SG B:CYS29 2.2 46.1 1.0
SG B:CYS26 2.3 63.1 1.0
SG B:CYS5 2.3 61.5 1.0
CB B:CYS29 2.8 39.0 1.0
CB B:CYS26 2.9 46.8 1.0
SG B:CYS8 3.0 82.8 1.0
CB B:CYS8 3.1 75.9 1.0
CB B:CYS5 3.3 68.5 1.0
N B:CYS26 3.6 54.5 1.0
CA B:CYS26 3.8 56.7 1.0
N B:CYS8 3.9 75.0 1.0
CA B:CYS29 4.0 40.3 1.0
N B:CYS29 4.1 41.6 1.0
CA B:CYS8 4.1 76.6 1.0
CB B:LEU7 4.4 76.1 1.0
CA B:GLY99 4.5 55.7 1.0
C B:CYS26 4.5 58.7 1.0
N B:GLY99 4.5 54.1 1.0
O B:CYS26 4.5 55.5 1.0
CA B:CYS5 4.7 75.2 1.0
C B:LEU7 4.7 72.0 1.0
CB B:SER10 4.8 60.8 1.0
C B:LEU25 4.8 53.5 1.0
N B:LEU7 5.0 66.9 1.0
CA B:LEU7 5.0 74.0 1.0
C B:GLY99 5.0 56.6 1.0

Zinc binding site 3 out of 6 in 5rl7

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Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:72.3
occ:1.00
 ND1 B:HIS75 2.2 87.5 1.0
SG B:CYS50 2.2 59.3 1.0
SG B:CYS55 2.3 68.6 1.0
SG B:CYS72 2.7 59.7 1.0
CG B:HIS75 3.0 84.3 1.0
CB B:CYS55 3.0 73.6 1.0
CE1 B:HIS75 3.1 89.9 1.0
CB B:CYS50 3.2 64.9 1.0
CB B:HIS75 3.3 77.6 1.0
CB B:CYS72 3.5 59.2 1.0
CB B:ALA52 3.8 99.5 1.0
N B:CYS72 3.9 58.1 1.0
CD2 B:HIS75 4.0 87.7 1.0
NE2 B:HIS75 4.0 91.8 1.0
CA B:CYS72 4.3 62.0 1.0
N B:HIS75 4.3 66.5 1.0
CA B:HIS75 4.4 73.4 1.0
CA B:CYS55 4.5 75.9 1.0
CA B:CYS50 4.6 65.4 1.0
CG2 B:VAL57 4.7 72.5 1.0
CB B:VAL57 4.8 74.5 1.0
C B:TYR71 4.9 62.7 1.0
C B:CYS72 4.9 65.8 1.0

Zinc binding site 4 out of 6 in 5rl7

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Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:44.9
occ:1.00
 ND1 A:HIS75 2.1 42.4 1.0
SG A:CYS55 2.2 42.4 1.0
SG A:CYS50 2.2 44.0 1.0
SG A:CYS72 2.5 47.5 1.0
CE1 A:HIS75 3.1 43.6 1.0
CG A:HIS75 3.1 40.1 1.0
CB A:CYS50 3.2 49.6 1.0
CB A:CYS55 3.2 46.1 1.0
CB A:CYS72 3.3 47.1 1.0
CB A:HIS75 3.4 39.9 1.0
N A:CYS72 3.8 43.5 1.0
CA A:CYS72 4.2 45.0 1.0
CB A:ALA52 4.2 48.0 1.0
NE2 A:HIS75 4.2 41.5 1.0
CD2 A:HIS75 4.2 39.4 1.0
CA A:CYS55 4.6 49.0 1.0
CA A:CYS50 4.6 47.3 1.0
CG2 A:VAL57 4.6 49.2 1.0
CA A:HIS75 4.7 40.8 1.0
N A:HIS75 4.7 44.1 1.0
C A:CYS72 4.8 49.7 1.0
O A:CYS72 4.8 44.9 1.0
CB A:VAL57 4.9 49.4 1.0
C A:TYR71 5.0 39.0 1.0

Zinc binding site 5 out of 6 in 5rl7

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Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:54.3
occ:1.00
 NE2 A:HIS33 1.7 25.1 1.0
ND1 A:HIS39 2.2 63.0 1.0
SG A:CYS16 2.2 67.1 1.0
SG A:CYS19 2.3 48.7 1.0
CE1 A:HIS33 2.7 34.8 1.0
CD2 A:HIS33 2.7 37.0 1.0
CG A:HIS39 3.1 64.5 1.0
CE1 A:HIS39 3.1 60.2 1.0
CB A:CYS16 3.2 62.6 1.0
N A:CYS19 3.3 52.8 1.0
CB A:HIS39 3.4 58.1 1.0
CB A:CYS19 3.6 39.8 1.0
ND1 A:HIS33 3.8 38.3 1.0
CG A:HIS33 3.8 37.9 1.0
CA A:CYS19 3.9 48.1 1.0
CB A:ALA18 3.9 67.0 1.0
C A:ALA18 4.2 62.5 1.0
NE2 A:HIS39 4.2 63.2 1.0
CD2 A:HIS39 4.2 64.2 1.0
CA A:ALA18 4.5 63.8 1.0
CB A:ALA110 4.6 58.9 1.0
CA A:CYS16 4.6 62.7 1.0
N A:ALA18 4.7 55.6 1.0
CA A:HIS39 4.9 57.4 1.0

Zinc binding site 6 out of 6 in 5rl7

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Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364321922 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:79.7
occ:1.00
 SG A:CYS5 2.0 88.5 1.0
SG A:CYS29 2.5 72.7 1.0
SG A:CYS26 2.7 79.7 1.0
SG A:CYS8 2.8 0.6 1.0
CB A:CYS26 3.1 67.5 1.0
CB A:CYS5 3.2 90.5 1.0
CB A:CYS29 3.2 78.0 1.0
CB A:CYS8 3.5 0.2 1.0
N A:CYS26 3.6 65.7 1.0
N A:CYS8 3.6 0.9 1.0
CA A:CYS26 3.9 69.1 1.0
CA A:CYS8 4.0 98.6 1.0
CB A:LEU7 4.3 99.9 1.0
C A:CYS8 4.4 92.2 1.0
CA A:CYS29 4.4 78.7 1.0
N A:CYS29 4.5 78.6 1.0
CA A:CYS5 4.5 90.1 1.0
O A:CYS5 4.5 85.3 1.0
C A:LEU7 4.6 99.4 1.0
N A:ASN9 4.7 92.8 1.0
C A:CYS5 4.8 91.5 1.0
C A:LEU25 4.8 64.5 1.0
N A:LEU7 4.8 87.2 1.0
C A:CYS26 4.8 69.2 1.0
CA A:LEU7 4.8 96.0 1.0
CB A:SER10 4.9 77.2 1.0
O A:CYS8 4.9 75.0 1.0
N A:SER10 5.0 87.8 1.0

Reference:

J.A.Newman, Y.Yosaatmadja, A.Douangamath, A.Aimon, A.J.Powell, A.Dias, D.Fearon, L.Dunnett, J.Brandao-Neto, T.Krojer, R.Skyner, T.Gorrie-Stone, W.Thompson, F.Von Delft, C.H.Arrowsmith, A.Edwards, C.Bountra, O.Gileadi. Pandda Analysis Group Deposition To Be Published.
Page generated: Wed Dec 16 06:53:24 2020

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