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Zinc in PDB 5rll: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z425387594

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z425387594

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z425387594:
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 Z425387594, PDB code: 5rll 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) 81.62 / 2.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.279, 70.220, 85.490, 102.36, 96.23, 112.60
R / Rfree (%) 21.5 / 26.7

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 Z425387594 (pdb code 5rll). 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 Z425387594, PDB code: 5rll:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rll

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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 Z425387594


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 Z425387594 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:59.8
occ:1.00
 SG A:CYS50 2.1 55.2 1.0
SG A:CYS55 2.2 57.2 1.0
ND1 A:HIS75 2.3 64.1 1.0
SG A:CYS72 2.4 52.5 1.0
CE1 A:HIS75 3.2 64.7 1.0
CB A:CYS50 3.2 60.4 1.0
CB A:CYS55 3.3 58.5 1.0
CB A:CYS72 3.3 56.6 1.0
CG A:HIS75 3.3 57.7 1.0
CB A:HIS75 3.7 56.5 1.0
N A:CYS72 3.8 51.0 1.0
CA A:CYS72 4.2 56.0 1.0
CB A:ALA52 4.3 51.6 1.0
NE2 A:HIS75 4.3 57.1 1.0
CD2 A:HIS75 4.4 59.5 1.0
CA A:CYS50 4.6 57.7 1.0
CG2 A:VAL57 4.6 60.4 1.0
N A:HIS75 4.6 55.1 1.0
CA A:CYS55 4.7 64.7 1.0
CB A:VAL57 4.8 56.2 1.0
CA A:HIS75 4.8 54.3 1.0
C A:CYS72 4.9 65.2 1.0
C A:TYR71 5.0 47.7 1.0

Zinc binding site 2 out of 6 in 5rll

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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 Z425387594


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 Z425387594 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:50.2
occ:1.00
 NE2 A:HIS33 1.9 35.5 1.0
ND1 A:HIS39 2.1 62.6 1.0
SG A:CYS16 2.3 63.8 1.0
SG A:CYS19 2.4 57.6 1.0
CE1 A:HIS33 2.8 40.0 1.0
CG A:HIS39 3.0 69.0 1.0
CD2 A:HIS33 3.0 43.3 1.0
CE1 A:HIS39 3.1 68.3 1.0
N A:CYS19 3.1 49.8 1.0
CB A:HIS39 3.3 64.0 1.0
CB A:CYS16 3.4 65.6 1.0
CB A:CYS19 3.5 44.7 1.0
CA A:CYS19 3.7 49.1 1.0
ND1 A:HIS33 4.0 45.0 1.0
C A:ALA18 4.0 60.5 1.0
CG A:HIS33 4.1 46.4 1.0
CD2 A:HIS39 4.1 72.3 1.0
NE2 A:HIS39 4.1 67.0 1.0
CB A:ALA18 4.3 68.8 1.0
CB A:ALA110 4.4 55.7 1.0
CA A:ALA18 4.6 64.3 1.0
N A:ALA18 4.7 59.1 1.0
CA A:CYS16 4.8 64.7 1.0
CA A:HIS39 4.8 60.3 1.0
O A:ALA18 4.9 66.2 1.0
CE2 A:PHE106 4.9 50.5 1.0
CZ A:PHE106 5.0 54.6 1.0

Zinc binding site 3 out of 6 in 5rll

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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 Z425387594


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 Z425387594 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:95.3
occ:1.00
 SG A:CYS5 2.2 77.1 1.0
SG A:CYS26 2.2 81.8 1.0
SG A:CYS8 2.3 0.3 1.0
SG A:CYS29 2.5 83.6 1.0
CB A:CYS29 3.1 88.5 1.0
CB A:CYS26 3.1 78.6 1.0
CB A:CYS5 3.5 78.9 1.0
CB A:CYS8 3.7 0.3 1.0
N A:CYS26 3.8 74.8 1.0
N A:CYS8 3.8 98.9 1.0
CA A:CYS26 3.9 81.2 1.0
CA A:CYS8 4.3 0.5 1.0
CA A:CYS29 4.3 82.9 1.0
N A:CYS29 4.3 83.5 1.0
CB A:LEU7 4.3 94.4 1.0
O A:CYS26 4.5 0.2 1.0
C A:CYS26 4.6 93.0 1.0
C A:LEU7 4.7 90.2 1.0
CA A:CYS5 4.8 83.4 1.0
C A:CYS8 4.8 98.8 1.0
CA A:LEU7 4.9 84.7 1.0
N A:LEU7 4.9 72.2 1.0
CB A:SER10 4.9 81.7 1.0
C A:LEU25 5.0 73.0 1.0
O A:CYS5 5.0 83.9 1.0

Zinc binding site 4 out of 6 in 5rll

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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 Z425387594


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 Z425387594 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:43.6
occ:1.00
 NE2 B:HIS33 2.0 37.6 1.0
SG B:CYS16 2.2 48.3 1.0
ND1 B:HIS39 2.2 60.7 1.0
SG B:CYS19 2.5 49.0 1.0
CD2 B:HIS33 2.9 37.6 1.0
CG B:HIS39 3.0 63.2 1.0
CE1 B:HIS33 3.0 40.2 1.0
CE1 B:HIS39 3.2 60.8 1.0
CB B:HIS39 3.2 59.3 1.0
CB B:CYS19 3.4 43.9 1.0
N B:CYS19 3.4 61.4 1.0
CB B:CYS16 3.4 55.5 1.0
CA B:CYS19 3.8 50.8 1.0
CG B:HIS33 4.1 40.7 1.0
CD2 B:HIS39 4.1 59.6 1.0
ND1 B:HIS33 4.1 37.5 1.0
NE2 B:HIS39 4.2 61.1 1.0
C B:ALA18 4.3 62.0 1.0
CB B:ALA18 4.5 61.1 1.0
CB B:ALA110 4.5 41.3 1.0
CA B:HIS39 4.7 53.0 1.0
CA B:ALA18 4.8 61.3 1.0
CA B:CYS16 4.8 59.5 1.0
N B:ALA18 4.8 59.6 1.0
C B:CYS16 5.0 54.5 1.0

Zinc binding site 5 out of 6 in 5rll

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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 Z425387594


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 Z425387594 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:74.9
occ:1.00
 SG B:CYS5 2.1 72.9 1.0
SG B:CYS26 2.1 80.2 1.0
SG B:CYS29 2.4 59.0 1.0
CB B:CYS29 2.9 63.8 1.0
CB B:CYS26 3.1 62.2 1.0
CB B:CYS8 3.2 85.7 1.0
SG B:CYS8 3.3 83.1 1.0
CB B:CYS5 3.4 84.3 1.0
N B:CYS26 3.7 77.7 1.0
N B:CYS8 3.7 90.1 1.0
CA B:CYS26 3.9 75.3 1.0
CA B:CYS8 4.0 86.4 1.0
CA B:CYS29 4.2 61.3 1.0
N B:CYS29 4.3 65.6 1.0
CB B:LEU7 4.3 96.5 1.0
O B:CYS26 4.3 61.6 1.0
C B:LEU7 4.4 87.8 1.0
C B:CYS26 4.5 72.9 1.0
CA B:CYS5 4.7 84.8 1.0
CA B:LEU7 4.7 90.3 1.0
OG B:SER10 4.8 69.8 1.0
N B:LEU7 4.8 79.8 1.0
N B:GLY99 4.8 75.0 1.0
C B:LEU25 4.8 75.1 1.0
CA B:GLY99 4.9 70.6 1.0
CB B:SER10 4.9 75.2 1.0
C B:CYS8 4.9 78.7 1.0
N B:ASN9 5.0 77.3 1.0

Zinc binding site 6 out of 6 in 5rll

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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 Z425387594


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 Z425387594 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:85.0
occ:1.00
 SG B:CYS50 2.1 81.8 1.0
SG B:CYS55 2.3 79.5 1.0
ND1 B:HIS75 2.4 87.3 1.0
SG B:CYS72 2.7 65.5 1.0
CB B:CYS50 3.1 89.6 1.0
CB B:CYS55 3.2 87.6 1.0
CG B:HIS75 3.2 83.3 1.0
CB B:HIS75 3.4 82.1 1.0
CE1 B:HIS75 3.4 89.0 1.0
CB B:CYS72 3.5 67.5 1.0
N B:CYS72 3.8 65.4 1.0
CB B:ALA52 4.0 99.5 1.0
CA B:CYS72 4.2 68.2 1.0
CD2 B:HIS75 4.4 88.7 1.0
N B:HIS75 4.4 71.7 1.0
NE2 B:HIS75 4.5 87.0 1.0
CA B:CYS50 4.5 90.8 1.0
CA B:HIS75 4.5 79.7 1.0
CG2 B:VAL57 4.5 98.8 1.0
CA B:CYS55 4.6 94.7 1.0
CB B:VAL57 4.8 0.6 1.0
C B:CYS72 4.9 75.3 1.0
C B:TYR71 4.9 70.5 1.0
N B:ALA52 5.0 97.3 1.0
C B:CYS50 5.0 98.3 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: Mon Oct 28 04:00:42 2024

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