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Zinc in PDB 5rlr: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z822382694

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z822382694

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z822382694:
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 Z822382694, PDB code: 5rlr 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) 81.66 / 2.32
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.250, 70.242, 85.595, 102.48, 96.28, 112.50
R / Rfree (%) 20.9 / 28.3

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 Z822382694 (pdb code 5rlr). 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 Z822382694, PDB code: 5rlr:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlr

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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 Z822382694


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 Z822382694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:54.2
occ:1.00
 SG A:CYS55 2.1 48.7 1.0
SG A:CYS50 2.2 59.6 1.0
ND1 A:HIS75 2.3 57.9 1.0
SG A:CYS72 2.4 53.1 1.0
CB A:CYS55 3.2 54.2 1.0
CB A:CYS50 3.2 68.1 1.0
CE1 A:HIS75 3.2 60.4 1.0
CG A:HIS75 3.2 51.8 1.0
CB A:CYS72 3.4 52.4 1.0
CB A:HIS75 3.6 48.0 1.0
N A:CYS72 3.9 50.0 1.0
CB A:ALA52 4.2 48.2 1.0
CA A:CYS72 4.2 53.1 1.0
NE2 A:HIS75 4.3 54.5 1.0
CD2 A:HIS75 4.3 54.6 1.0
N A:HIS75 4.5 49.9 1.0
CA A:CYS55 4.6 58.0 1.0
CG2 A:VAL57 4.6 57.9 1.0
CA A:CYS50 4.6 63.8 1.0
CA A:HIS75 4.7 45.8 1.0
CB A:VAL57 4.8 56.1 1.0
C A:CYS72 4.9 61.9 1.0
CB A:SER74 5.0 60.1 1.0

Zinc binding site 2 out of 6 in 5rlr

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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 Z822382694


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 Z822382694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:50.8
occ:1.00
 NE2 A:HIS33 2.0 35.0 1.0
ND1 A:HIS39 2.2 68.4 1.0
SG A:CYS16 2.2 76.5 1.0
SG A:CYS19 2.4 53.2 1.0
CE1 A:HIS33 2.8 39.6 1.0
CG A:HIS39 3.1 70.3 1.0
CE1 A:HIS39 3.1 72.8 1.0
N A:CYS19 3.1 53.4 1.0
CD2 A:HIS33 3.2 42.6 1.0
CB A:CYS19 3.4 48.3 1.0
CB A:CYS16 3.4 72.1 1.0
CB A:HIS39 3.4 71.4 1.0
CA A:CYS19 3.6 53.4 1.0
ND1 A:HIS33 4.0 45.0 1.0
C A:ALA18 4.1 64.7 1.0
NE2 A:HIS39 4.1 71.2 1.0
CD2 A:HIS39 4.1 74.0 1.0
CG A:HIS33 4.2 45.4 1.0
CB A:ALA18 4.2 79.4 1.0
CB A:ALA110 4.5 57.3 1.0
CA A:ALA18 4.6 72.6 1.0
N A:ALA18 4.7 70.1 1.0
CA A:CYS16 4.7 72.1 1.0
CA A:HIS39 4.9 69.1 1.0

Zinc binding site 3 out of 6 in 5rlr

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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 Z822382694


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 Z822382694 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:81.0
occ:1.00
 SG A:CYS5 2.0 81.0 1.0
SG A:CYS29 2.3 72.7 1.0
SG A:CYS8 2.4 88.6 1.0
SG A:CYS26 2.6 85.5 1.0
CB A:CYS5 3.0 79.4 1.0
CB A:CYS29 3.1 83.5 1.0
CB A:CYS26 3.2 74.7 1.0
CB A:CYS8 3.6 85.0 1.0
N A:CYS26 3.8 78.8 1.0
N A:CYS8 3.9 81.8 1.0
CA A:CYS26 4.1 77.0 1.0
CA A:CYS8 4.3 86.4 1.0
CB A:LEU7 4.4 84.5 1.0
CA A:CYS29 4.4 81.8 1.0
CA A:CYS5 4.4 80.1 1.0
N A:CYS29 4.5 85.7 1.0
C A:LEU7 4.5 78.5 1.0
CB A:SER10 4.6 81.0 1.0
N A:LEU7 4.7 65.8 1.0
O A:CYS26 4.7 80.7 1.0
CA A:LEU7 4.8 78.2 1.0
C A:CYS26 4.8 78.3 1.0
C A:CYS8 4.8 88.4 1.0
C A:CYS5 4.8 75.7 1.0
O A:CYS5 4.8 75.4 1.0
N A:ASN9 4.9 91.5 1.0
OG A:SER10 4.9 69.3 1.0
N A:SER10 4.9 92.5 1.0
C A:LEU25 5.0 79.3 1.0

Zinc binding site 4 out of 6 in 5rlr

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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 Z822382694


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 Z822382694 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:45.7
occ:1.00
 NE2 B:HIS33 1.9 42.2 1.0
SG B:CYS16 2.2 45.4 1.0
ND1 B:HIS39 2.3 56.1 1.0
SG B:CYS19 2.5 52.2 1.0
CE1 B:HIS33 2.8 43.0 1.0
CD2 B:HIS33 3.0 45.0 1.0
CG B:HIS39 3.0 60.7 1.0
CE1 B:HIS39 3.2 58.4 1.0
CB B:HIS39 3.3 61.3 1.0
N B:CYS19 3.4 54.2 1.0
CB B:CYS16 3.5 50.0 1.0
CB B:CYS19 3.5 49.4 1.0
CA B:CYS19 3.8 49.8 1.0
ND1 B:HIS33 4.0 41.9 1.0
CD2 B:HIS39 4.1 56.7 1.0
CG B:HIS33 4.1 47.2 1.0
NE2 B:HIS39 4.1 61.2 1.0
C B:ALA18 4.4 54.3 1.0
CB B:ALA18 4.4 50.2 1.0
CB B:ALA110 4.5 39.0 1.0
CA B:HIS39 4.8 55.6 1.0
CA B:ALA18 4.8 53.0 1.0
CA B:CYS16 4.8 52.9 1.0
N B:ALA18 4.9 54.6 1.0

Zinc binding site 5 out of 6 in 5rlr

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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 Z822382694


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 Z822382694 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:78.7
occ:1.00
 SG B:CYS26 1.9 76.4 1.0
SG B:CYS5 2.0 73.8 1.0
SG B:CYS29 2.3 57.7 1.0
CB B:CYS29 2.7 57.9 1.0
CB B:CYS8 3.0 80.9 1.0
CB B:CYS5 3.2 85.9 1.0
CB B:CYS26 3.3 67.3 1.0
SG B:CYS8 3.5 74.2 1.0
N B:CYS26 3.6 73.6 1.0
N B:CYS8 3.8 82.0 1.0
CA B:CYS26 4.0 75.5 1.0
CA B:CYS29 4.0 58.9 1.0
CA B:CYS8 4.1 80.8 1.0
N B:CYS29 4.2 60.0 1.0
O B:CYS26 4.3 63.5 1.0
CB B:LEU7 4.4 79.2 1.0
C B:LEU7 4.6 79.7 1.0
C B:CYS26 4.6 73.8 1.0
CA B:CYS5 4.6 84.7 1.0
CB B:SER10 4.7 70.8 1.0
OG B:SER100 4.8 56.1 1.0
CA B:GLY99 4.8 65.9 1.0
C B:LEU25 4.8 72.8 1.0
N B:LEU7 4.8 65.4 1.0
CA B:LEU7 4.8 77.6 1.0
N B:GLY99 4.9 69.7 1.0
OG B:SER10 5.0 68.9 1.0

Zinc binding site 6 out of 6 in 5rlr

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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 Z822382694


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 Z822382694 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:78.7
occ:1.00
 SG B:CYS50 2.1 88.5 1.0
SG B:CYS55 2.3 94.1 1.0
SG B:CYS72 2.7 57.8 1.0
ND1 B:HIS75 2.7 86.2 1.0
CB B:CYS50 2.9 93.8 1.0
CB B:CYS55 3.2 99.0 1.0
CB B:CYS72 3.4 61.4 1.0
CG B:HIS75 3.5 86.1 1.0
CB B:HIS75 3.6 83.0 1.0
N B:CYS72 3.7 60.2 1.0
CE1 B:HIS75 3.7 88.9 1.0
CB B:ALA52 4.1 92.5 1.0
CA B:CYS72 4.1 63.7 1.0
CA B:CYS50 4.4 85.6 1.0
CG2 B:VAL57 4.5 86.6 1.0
N B:HIS75 4.5 70.0 1.0
CB B:VAL57 4.6 87.6 1.0
CD2 B:HIS75 4.6 88.7 1.0
CA B:CYS55 4.6 0.5 1.0
CA B:HIS75 4.7 78.1 1.0
NE2 B:HIS75 4.7 90.3 1.0
C B:TYR71 4.8 60.9 1.0
C B:CYS72 4.9 67.8 1.0
CA B:TYR71 5.0 70.3 1.0
N B:ALA52 5.0 91.7 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 04:06:32 2024

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