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Zinc in PDB 5rm8: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1614545742

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1614545742

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1614545742:
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 Z1614545742, PDB code: 5rm8 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) 81.46 / 2.14
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.246, 70.275, 85.494, 102.90, 96.06, 112.34
R / Rfree (%) 16.7 / 24.8

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 Z1614545742 (pdb code 5rm8). 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 Z1614545742, PDB code: 5rm8:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm8

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:69.1
occ:1.00
 ND1 A:HIS75 2.3 60.5 1.0
SG A:CYS55 2.3 76.2 1.0
SG A:CYS50 2.4 65.0 1.0
SG A:CYS72 2.8 67.8 1.0
CB A:CYS55 3.2 78.1 1.0
CE1 A:HIS75 3.2 59.9 1.0
CG A:HIS75 3.3 60.6 1.0
CB A:CYS50 3.3 69.4 1.0
CB A:CYS72 3.4 69.4 1.0
CB A:HIS75 3.6 59.5 1.0
N A:CYS72 3.8 64.8 1.0
CA A:CYS72 4.2 66.5 1.0
CB A:ALA52 4.2 61.7 1.0
NE2 A:HIS75 4.4 58.9 1.0
CD2 A:HIS75 4.4 58.9 1.0
CG2 A:VAL57 4.5 70.3 1.0
N A:HIS75 4.5 64.3 1.0
CA A:CYS55 4.6 79.3 1.0
CB A:VAL57 4.7 70.7 1.0
CA A:HIS75 4.7 61.6 1.0
CA A:CYS50 4.7 71.3 1.0
C A:TYR71 5.0 60.2 1.0
C A:CYS72 5.0 69.9 1.0

Zinc binding site 2 out of 6 in 5rm8

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:67.8
occ:1.00
 ND1 A:HIS39 2.1 70.0 1.0
NE2 A:HIS33 2.1 60.5 1.0
SG A:CYS16 2.2 82.0 1.0
SG A:CYS19 2.4 71.9 1.0
CE1 A:HIS33 3.0 60.8 1.0
CE1 A:HIS39 3.0 69.8 1.0
CG A:HIS39 3.1 71.8 1.0
CD2 A:HIS33 3.2 62.7 1.0
CB A:CYS16 3.4 80.8 1.0
CB A:HIS39 3.4 69.7 1.0
CB A:CYS19 3.4 68.7 1.0
N A:CYS19 3.5 69.2 1.0
CA A:CYS19 3.8 71.6 1.0
ND1 A:HIS33 4.1 62.2 1.0
C A:ALA18 4.1 77.0 1.0
NE2 A:HIS39 4.2 72.4 1.0
CD2 A:HIS39 4.2 73.4 1.0
CG A:HIS33 4.2 64.6 1.0
CB A:ALA110 4.4 64.5 1.0
CB A:ALA18 4.4 80.1 1.0
CA A:ALA18 4.6 78.3 1.0
CA A:CYS16 4.7 81.9 1.0
N A:ALA18 4.7 78.6 1.0
O A:ALA18 4.9 78.9 1.0
CA A:HIS39 4.9 69.6 1.0
CE2 A:PHE106 5.0 77.8 1.0

Zinc binding site 3 out of 6 in 5rm8

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.2
occ:1.00
 SG A:CYS5 2.3 99.5 1.0
SG A:CYS26 2.4 99.3 1.0
SG A:CYS8 2.4 0.7 1.0
SG A:CYS29 2.4 99.7 1.0
CB A:CYS29 3.1 93.9 1.0
CB A:CYS8 3.5 0.9 1.0
CB A:CYS26 3.5 97.0 1.0
CB A:CYS5 3.5 98.7 1.0
N A:CYS8 3.6 0.6 1.0
N A:CYS26 4.0 93.7 1.0
CA A:CYS8 4.0 0.4 1.0
N A:CYS29 4.2 94.1 1.0
CA A:CYS29 4.2 87.9 1.0
CA A:CYS26 4.3 98.8 1.0
CB A:LEU7 4.4 0.1 1.0
C A:LEU7 4.5 0.8 1.0
C A:CYS8 4.7 0.2 1.0
CA A:LEU7 4.8 0.5 1.0
N A:LEU7 4.8 0.8 1.0
OG A:SER10 4.9 0.1 1.0
CA A:CYS5 4.9 98.4 1.0
C A:CYS26 4.9 99.4 1.0
CB A:SER10 4.9 0.2 1.0
N A:ASN9 5.0 1.0 1.0
O A:CYS26 5.0 99.0 1.0

Zinc binding site 4 out of 6 in 5rm8

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:42.6
occ:1.00
 NE2 B:HIS33 2.0 54.5 1.0
ND1 B:HIS39 2.1 53.9 1.0
SG B:CYS16 2.2 52.8 1.0
SG B:CYS19 2.5 55.3 1.0
CE1 B:HIS33 3.0 53.8 1.0
CG B:HIS39 3.1 56.5 1.0
CE1 B:HIS39 3.1 52.7 1.0
CD2 B:HIS33 3.1 55.4 1.0
CB B:HIS39 3.4 56.5 1.0
CB B:CYS16 3.4 58.5 1.0
N B:CYS19 3.5 60.4 1.0
CB B:CYS19 3.5 59.4 1.0
CA B:CYS19 3.8 60.9 1.0
ND1 B:HIS33 4.1 55.6 1.0
C B:ALA18 4.2 57.8 1.0
NE2 B:HIS39 4.2 55.6 1.0
CD2 B:HIS39 4.2 55.8 1.0
CG B:HIS33 4.2 56.0 1.0
CB B:ALA18 4.4 51.2 1.0
CB B:ALA110 4.5 48.7 1.0
CA B:ALA18 4.6 57.1 1.0
N B:ALA18 4.7 58.5 1.0
CA B:CYS16 4.7 56.9 1.0
CA B:HIS39 4.8 57.7 1.0
O B:ALA18 4.9 60.6 1.0

Zinc binding site 5 out of 6 in 5rm8

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:79.4
occ:1.00
 SG B:CYS5 2.4 76.2 1.0
SG B:CYS26 2.4 74.0 1.0
SG B:CYS29 2.4 76.6 1.0
CB B:CYS8 2.9 97.5 1.0
CB B:CYS29 3.0 70.2 1.0
SG B:CYS8 3.1 0.3 1.0
CB B:CYS26 3.5 71.9 1.0
CB B:CYS5 3.5 81.7 1.0
N B:CYS8 3.7 94.6 1.0
N B:CYS26 3.9 70.3 1.0
CA B:CYS8 3.9 93.1 1.0
N B:CYS29 4.1 69.3 1.0
CA B:CYS29 4.1 66.4 1.0
CA B:CYS26 4.2 70.6 1.0
CB B:LEU7 4.5 88.6 1.0
C B:LEU7 4.6 90.1 1.0
N B:GLY99 4.8 97.2 1.0
OG B:SER10 4.8 85.0 1.0
C B:CYS26 4.8 73.3 1.0
O B:CYS26 4.9 76.3 1.0
CA B:GLY99 4.9 95.6 1.0
CB B:SER10 4.9 85.9 1.0
CA B:LEU7 4.9 86.8 1.0
CA B:CYS5 4.9 81.2 1.0
N B:LEU7 4.9 84.3 1.0
C B:CYS8 5.0 92.0 1.0

Zinc binding site 6 out of 6 in 5rm8

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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 Z1614545742


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 Z1614545742 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:95.9
occ:1.00
 ND1 B:HIS75 2.2 92.2 1.0
SG B:CYS50 2.2 83.1 1.0
SG B:CYS55 2.4 0.0 1.0
SG B:CYS72 2.9 87.0 1.0
CB B:CYS55 3.2 0.5 1.0
CG B:HIS75 3.2 90.6 1.0
CE1 B:HIS75 3.2 91.9 1.0
CB B:CYS50 3.2 86.0 1.0
CB B:HIS75 3.5 89.0 1.0
CB B:CYS72 3.5 83.8 1.0
N B:CYS72 3.8 82.1 1.0
CB B:ALA52 4.1 1.0 1.0
CA B:CYS72 4.2 84.0 1.0
NE2 B:HIS75 4.3 91.4 1.0
CD2 B:HIS75 4.3 92.0 1.0
N B:HIS75 4.5 90.6 1.0
CA B:HIS75 4.6 89.6 1.0
CG2 B:VAL57 4.6 93.6 1.0
CA B:CYS55 4.6 0.1 1.0
CA B:CYS50 4.7 86.2 1.0
CB B:VAL57 4.8 94.8 1.0
C B:TYR71 4.9 81.3 1.0
C B:CYS72 5.0 84.3 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: Thu Aug 21 07:24:02 2025

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