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Zinc in PDB 5rl8: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177:
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 Z53825177, PDB code: 5rl8 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) 81.24 / 2.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.112, 70.206, 85.095, 102.61, 95.93, 112.44
R / Rfree (%) 20.9 / 27

Other elements in 5rl8:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177 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 Z53825177 (pdb code 5rl8). 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 Z53825177, PDB code: 5rl8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rl8

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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 Z53825177


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 Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:40.1
occ:1.00
 NE2 B:HIS33 2.1 35.2 1.0
SG B:CYS16 2.1 43.6 1.0
ND1 B:HIS39 2.2 52.0 1.0
SG B:CYS19 2.5 41.4 1.0
CD2 B:HIS33 3.0 35.3 1.0
CG B:HIS39 3.0 54.5 1.0
CE1 B:HIS39 3.1 56.2 1.0
CB B:CYS16 3.2 46.5 1.0
CE1 B:HIS33 3.2 38.7 1.0
CB B:HIS39 3.3 51.9 1.0
CB B:CYS19 3.4 39.2 1.0
N B:CYS19 3.5 53.0 1.0
CA B:CYS19 3.8 46.0 1.0
CD2 B:HIS39 4.2 50.1 1.0
NE2 B:HIS39 4.2 52.0 1.0
CG B:HIS33 4.2 41.1 1.0
ND1 B:HIS33 4.3 37.5 1.0
C B:ALA18 4.4 50.5 1.0
CB B:ALA110 4.5 34.6 1.0
CB B:ALA18 4.5 46.6 1.0
CA B:CYS16 4.6 51.1 1.0
CA B:HIS39 4.8 49.3 1.0
CA B:ALA18 4.8 48.8 1.0
N B:ALA18 4.8 50.0 1.0
C B:CYS16 4.9 47.9 1.0

Zinc binding site 2 out of 6 in 5rl8

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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 Z53825177


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 Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:65.5
occ:1.00
 SG B:CYS5 1.8 82.5 1.0
SG B:CYS26 2.1 84.2 1.0
SG B:CYS29 2.5 64.9 1.0
CB B:CYS29 2.9 58.7 1.0
CB B:CYS5 3.0 78.3 1.0
CB B:CYS26 3.0 60.4 1.0
CB B:CYS8 3.1 85.4 1.0
SG B:CYS8 3.3 84.3 1.0
N B:CYS26 3.5 78.8 1.0
CA B:CYS26 3.7 75.3 1.0
N B:CYS8 3.8 86.2 1.0
N B:CYS29 4.0 56.6 1.0
CA B:CYS29 4.1 55.4 1.0
CA B:CYS8 4.1 90.1 1.0
O B:CYS26 4.2 74.5 1.0
CB B:SER10 4.3 75.0 1.0
CA B:CYS5 4.3 81.2 1.0
C B:CYS26 4.4 73.4 1.0
CB B:LEU7 4.6 96.9 1.0
N B:GLY99 4.6 71.1 1.0
CA B:GLY99 4.6 66.8 1.0
OG B:SER10 4.7 83.0 1.0
O B:CYS5 4.7 73.6 1.0
C B:LEU25 4.7 70.8 1.0
C B:LEU7 4.8 77.8 1.0
C B:CYS5 4.8 77.4 1.0
N B:LEU7 4.9 76.8 1.0

Zinc binding site 3 out of 6 in 5rl8

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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 Z53825177


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 Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:78.6
occ:1.00
 SG B:CYS55 2.3 82.0 1.0
ND1 B:HIS75 2.5 86.0 1.0
SG B:CYS50 2.5 73.4 1.0
SG B:CYS72 2.7 67.3 1.0
CB B:CYS55 3.1 81.9 1.0
CE1 B:HIS75 3.2 83.2 1.0
CB B:CYS50 3.3 77.3 1.0
CB B:CYS72 3.3 70.6 1.0
CG B:HIS75 3.4 81.6 1.0
CB B:HIS75 3.8 79.7 1.0
N B:CYS72 3.9 57.9 1.0
CG2 B:VAL57 4.1 80.5 1.0
CB B:ALA52 4.1 96.1 1.0
CA B:CYS72 4.2 67.2 1.0
NE2 B:HIS75 4.3 79.5 1.0
CD2 B:HIS75 4.4 81.6 1.0
CB B:VAL57 4.5 83.1 1.0
CA B:CYS55 4.5 85.2 1.0
N B:HIS75 4.7 70.2 1.0
CA B:CYS50 4.8 75.7 1.0
CA B:HIS75 4.9 78.0 1.0
C B:CYS72 4.9 72.6 1.0

Zinc binding site 4 out of 6 in 5rl8

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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 Z53825177


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 Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:58.1
occ:1.00
 ND1 A:HIS75 2.1 62.3 1.0
SG A:CYS55 2.2 60.1 1.0
SG A:CYS50 2.2 57.0 1.0
SG A:CYS72 2.5 61.0 1.0
CE1 A:HIS75 2.9 64.7 1.0
CB A:CYS72 3.1 57.1 1.0
CB A:CYS50 3.1 61.3 1.0
CB A:CYS55 3.2 56.3 1.0
CG A:HIS75 3.3 59.6 1.0
CB A:HIS75 3.8 57.3 1.0
N A:CYS72 3.8 52.4 1.0
CA A:CYS72 4.1 56.9 1.0
NE2 A:HIS75 4.1 57.3 1.0
CB A:ALA52 4.3 60.4 1.0
CD2 A:HIS75 4.3 58.6 1.0
CA A:CYS55 4.6 62.0 1.0
CA A:CYS50 4.6 59.2 1.0
N A:HIS75 4.7 57.3 1.0
CG2 A:VAL57 4.8 50.4 1.0
CB A:VAL57 4.8 49.7 1.0
C A:CYS72 4.8 62.5 1.0
CA A:HIS75 4.9 54.2 1.0
C A:TYR71 5.0 49.0 1.0

Zinc binding site 5 out of 6 in 5rl8

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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 Z53825177


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 Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:55.5
occ:1.00
 NE2 A:HIS33 1.7 29.2 1.0
ND1 A:HIS39 2.0 65.6 1.0
SG A:CYS16 2.3 71.0 1.0
SG A:CYS19 2.5 50.7 1.0
CE1 A:HIS33 2.7 31.4 1.0
CD2 A:HIS33 2.8 35.1 1.0
CE1 A:HIS39 3.0 71.6 1.0
CG A:HIS39 3.0 72.1 1.0
N A:CYS19 3.0 54.7 1.0
CB A:CYS16 3.4 63.6 1.0
CB A:HIS39 3.4 64.9 1.0
CB A:CYS19 3.4 44.0 1.0
CA A:CYS19 3.6 50.8 1.0
ND1 A:HIS33 3.8 33.8 1.0
CG A:HIS33 3.9 37.0 1.0
CB A:ALA18 4.0 73.4 1.0
NE2 A:HIS39 4.0 69.7 1.0
C A:ALA18 4.0 65.1 1.0
CD2 A:HIS39 4.1 75.9 1.0
CA A:ALA18 4.4 69.8 1.0
CB A:ALA110 4.5 54.5 1.0
N A:ALA18 4.6 65.2 1.0
CA A:CYS16 4.7 64.2 1.0
CA A:HIS39 4.8 59.8 1.0
C A:CYS16 5.0 61.8 1.0
CE2 A:PHE106 5.0 55.1 1.0
O A:CYS16 5.0 67.6 1.0

Zinc binding site 6 out of 6 in 5rl8

Go back to Zinc Binding Sites List in 5rl8
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53825177


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 Z53825177 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:95.4
occ:1.00
 SG A:CYS26 2.3 96.3 1.0
SG A:CYS5 2.4 82.3 1.0
SG A:CYS29 2.5 91.2 1.0
SG A:CYS8 2.6 0.1 1.0
CB A:CYS29 3.0 94.5 1.0
CB A:CYS26 3.3 80.7 1.0
CB A:CYS8 3.4 99.2 1.0
CB A:CYS5 3.7 87.2 1.0
N A:CYS8 3.9 0.1 1.0
N A:CYS26 4.0 79.1 1.0
CA A:CYS26 4.2 79.6 1.0
CA A:CYS29 4.2 83.6 1.0
CA A:CYS8 4.2 0.9 1.0
N A:CYS29 4.3 79.7 1.0
O A:CYS26 4.3 92.2 1.0
CB A:LEU7 4.3 97.4 1.0
C A:CYS26 4.6 87.1 1.0
C A:LEU7 4.7 96.4 1.0
CA A:LEU7 4.9 93.0 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: Mon Oct 28 03:54:46 2024

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