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Zinc in PDB 5rlz: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2293643386

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2293643386

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2293643386:
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 Z2293643386, PDB code: 5rlz 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 / 1.97
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.208, 70.390, 85.354, 102.74, 95.87, 112.42
R / Rfree (%) 22.2 / 27.3

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 Z2293643386 (pdb code 5rlz). 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 Z2293643386, PDB code: 5rlz:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlz

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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 Z2293643386


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 Z2293643386 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:43.0
occ:1.00
 SG B:CYS16 2.1 45.5 1.0
NE2 B:HIS33 2.1 33.2 1.0
ND1 B:HIS39 2.1 48.3 1.0
SG B:CYS19 2.5 46.5 1.0
CD2 B:HIS33 3.0 34.6 1.0
CG B:HIS39 3.0 53.4 1.0
CE1 B:HIS39 3.1 55.1 1.0
CB B:CYS16 3.2 50.6 1.0
CE1 B:HIS33 3.3 36.7 1.0
CB B:HIS39 3.3 48.6 1.0
CB B:CYS19 3.4 43.3 1.0
N B:CYS19 3.5 51.3 1.0
CA B:CYS19 3.9 48.3 1.0
CD2 B:HIS39 4.1 51.8 1.0
NE2 B:HIS39 4.1 54.4 1.0
CG B:HIS33 4.2 36.5 1.0
ND1 B:HIS33 4.3 34.4 1.0
C B:ALA18 4.4 53.2 1.0
CB B:ALA110 4.5 34.2 1.0
CB B:ALA18 4.6 44.0 1.0
CA B:CYS16 4.6 53.2 1.0
CA B:HIS39 4.8 47.9 1.0
N B:ALA18 4.8 50.4 1.0
CA B:ALA18 4.9 49.1 1.0
C B:CYS16 4.9 51.2 1.0

Zinc binding site 2 out of 6 in 5rlz

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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 Z2293643386


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 Z2293643386 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:72.9
occ:1.00
 SG B:CYS5 1.9 81.5 1.0
SG B:CYS26 2.3 86.9 1.0
SG B:CYS29 2.3 62.1 1.0
CB B:CYS26 2.8 66.8 1.0
CB B:CYS29 2.9 58.6 1.0
CB B:CYS5 3.0 86.5 1.0
SG B:CYS8 3.2 84.8 1.0
CB B:CYS8 3.2 89.6 1.0
N B:CYS26 3.4 76.8 1.0
CA B:CYS26 3.6 75.9 1.0
N B:CYS8 3.9 92.4 1.0
CA B:CYS29 4.1 56.4 1.0
N B:CYS29 4.2 58.5 1.0
CA B:CYS8 4.2 90.0 1.0
O B:CYS26 4.3 65.6 1.0
C B:CYS26 4.3 73.8 1.0
CA B:CYS5 4.4 86.9 1.0
CB B:SER10 4.4 73.5 1.0
C B:LEU25 4.6 69.8 1.0
O B:CYS5 4.7 70.2 1.0
CB B:LEU7 4.7 98.2 1.0
C B:CYS5 4.8 82.4 1.0
N B:GLY99 4.8 71.2 1.0
C B:LEU7 4.8 85.7 1.0
CA B:GLY99 4.9 66.9 1.0
OG B:SER10 4.9 76.3 1.0
N B:LEU7 5.0 82.2 1.0
N B:ASN9 5.0 82.2 1.0

Zinc binding site 3 out of 6 in 5rlz

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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 Z2293643386


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 Z2293643386 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:74.2
occ:1.00
 SG B:CYS50 2.3 69.7 1.0
SG B:CYS55 2.3 82.0 1.0
ND1 B:HIS75 2.6 87.2 1.0
SG B:CYS72 2.7 59.6 1.0
CB B:CYS55 3.0 89.0 1.0
CG B:HIS75 3.3 82.7 1.0
CB B:CYS50 3.3 73.9 1.0
CE1 B:HIS75 3.4 87.1 1.0
CB B:CYS72 3.4 62.6 1.0
CB B:HIS75 3.6 78.5 1.0
CB B:ALA52 3.9 90.8 1.0
N B:CYS72 3.9 56.3 1.0
CA B:CYS72 4.2 63.0 1.0
CD2 B:HIS75 4.3 83.8 1.0
NE2 B:HIS75 4.3 85.0 1.0
CG2 B:VAL57 4.4 72.6 1.0
CA B:CYS55 4.5 91.9 1.0
N B:HIS75 4.7 65.8 1.0
CB B:VAL57 4.7 75.9 1.0
CA B:HIS75 4.7 76.8 1.0
CA B:CYS50 4.7 74.9 1.0
C B:CYS72 5.0 70.0 1.0
C B:TYR71 5.0 58.5 1.0

Zinc binding site 4 out of 6 in 5rlz

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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 Z2293643386


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 Z2293643386 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:61.6
occ:1.00
 SG A:CYS55 2.1 59.5 1.0
ND1 A:HIS75 2.2 59.0 1.0
SG A:CYS50 2.3 59.2 1.0
SG A:CYS72 2.4 55.7 1.0
CE1 A:HIS75 3.1 59.2 1.0
CB A:CYS55 3.1 60.0 1.0
CB A:CYS50 3.2 62.2 1.0
CB A:CYS72 3.2 58.6 1.0
CG A:HIS75 3.3 56.3 1.0
CB A:HIS75 3.7 54.7 1.0
N A:CYS72 3.8 53.1 1.0
CA A:CYS72 4.1 57.1 1.0
NE2 A:HIS75 4.2 58.5 1.0
CB A:ALA52 4.3 57.8 1.0
CD2 A:HIS75 4.4 57.1 1.0
CA A:CYS55 4.5 64.0 1.0
CG2 A:VAL57 4.6 62.1 1.0
CA A:CYS50 4.6 59.9 1.0
N A:HIS75 4.7 56.2 1.0
CB A:VAL57 4.7 59.6 1.0
CA A:HIS75 4.8 53.8 1.0
C A:CYS72 4.9 64.0 1.0
CB A:SER74 4.9 64.7 1.0
C A:TYR71 5.0 47.6 1.0

Zinc binding site 5 out of 6 in 5rlz

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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 Z2293643386


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 Z2293643386 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:56.7
occ:1.00
 NE2 A:HIS33 1.7 31.7 1.0
ND1 A:HIS39 2.0 70.6 1.0
SG A:CYS16 2.2 82.5 1.0
SG A:CYS19 2.6 55.4 1.0
CE1 A:HIS33 2.7 36.8 1.0
CD2 A:HIS33 2.8 36.2 1.0
CE1 A:HIS39 3.0 76.0 1.0
CG A:HIS39 3.0 75.3 1.0
N A:CYS19 3.1 54.2 1.0
CB A:CYS16 3.3 73.4 1.0
CB A:HIS39 3.4 67.3 1.0
CB A:CYS19 3.6 46.2 1.0
CA A:CYS19 3.8 53.2 1.0
ND1 A:HIS33 3.8 39.2 1.0
CG A:HIS33 3.9 37.9 1.0
CB A:ALA18 3.9 64.7 1.0
C A:ALA18 4.1 63.7 1.0
NE2 A:HIS39 4.1 72.1 1.0
CD2 A:HIS39 4.2 75.1 1.0
CA A:ALA18 4.4 65.1 1.0
CB A:ALA110 4.5 62.0 1.0
N A:ALA18 4.6 61.6 1.0
CA A:CYS16 4.7 70.3 1.0
CA A:HIS39 4.8 64.3 1.0
CE2 A:PHE106 5.0 49.1 1.0

Zinc binding site 6 out of 6 in 5rlz

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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 Z2293643386


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 Z2293643386 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:89.2
occ:1.00
 SG A:CYS5 2.3 79.8 1.0
SG A:CYS29 2.4 82.6 1.0
SG A:CYS26 2.6 84.1 1.0
SG A:CYS8 2.8 0.3 1.0
CB A:CYS29 3.0 83.8 1.0
CB A:CYS26 3.0 78.0 1.0
CB A:CYS8 3.5 0.6 1.0
CB A:CYS5 3.7 86.2 1.0
N A:CYS26 3.8 74.1 1.0
N A:CYS8 3.9 0.1 1.0
CA A:CYS26 3.9 78.4 1.0
O A:CYS26 4.2 86.6 1.0
CA A:CYS29 4.3 80.3 1.0
CA A:CYS8 4.3 0.1 1.0
N A:CYS29 4.3 78.6 1.0
CB A:LEU7 4.4 99.3 1.0
C A:CYS26 4.5 87.9 1.0
C A:LEU7 4.8 97.7 1.0
CA A:CYS5 5.0 88.3 1.0
C A:CYS8 5.0 0.8 1.0
CA A:LEU7 5.0 93.5 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 07:21:00 2025

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