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Zinc in PDB 5rln: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788:
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 Z364328788, PDB code: 5rln 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) 62.34 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.108, 70.366, 85.925, 102.79, 96.70, 112.26
R / Rfree (%) 17.4 / 25.8

Other elements in 5rln:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788 also contains other interesting chemical elements:

Fluorine (F) 1 atom

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 Z364328788 (pdb code 5rln). 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 Z364328788, PDB code: 5rln:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rln

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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 Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:58.4
occ:1.00
 ND1 A:HIS75 2.3 53.5 1.0
SG A:CYS55 2.3 59.8 1.0
SG A:CYS50 2.4 62.3 1.0
SG A:CYS72 2.7 61.0 1.0
CG A:HIS75 3.2 53.4 1.0
CE1 A:HIS75 3.3 53.4 1.0
CB A:CYS50 3.3 66.5 1.0
CB A:CYS55 3.4 65.6 1.0
CB A:CYS72 3.4 61.5 1.0
CB A:HIS75 3.5 51.3 1.0
N A:CYS72 3.8 56.9 1.0
CA A:CYS72 4.2 59.0 1.0
CB A:ALA52 4.2 56.2 1.0
CD2 A:HIS75 4.4 52.5 1.0
NE2 A:HIS75 4.4 51.1 1.0
N A:HIS75 4.4 53.8 1.0
CG2 A:VAL57 4.5 60.7 1.0
CA A:HIS75 4.6 53.3 1.0
CB A:VAL57 4.7 63.8 1.0
CA A:CYS50 4.7 66.6 1.0
CA A:CYS55 4.8 68.3 1.0
C A:TYR71 4.9 53.6 1.0
C A:CYS72 4.9 61.5 1.0

Zinc binding site 2 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:69.5
occ:1.00
 NE2 A:HIS33 2.1 57.4 1.0
ND1 A:HIS39 2.2 79.5 1.0
SG A:CYS19 2.3 71.3 1.0
SG A:CYS16 2.3 86.1 1.0
CE1 A:HIS33 2.9 60.5 1.0
CG A:HIS39 3.2 80.2 1.0
CE1 A:HIS39 3.2 80.5 1.0
CD2 A:HIS33 3.2 63.2 1.0
CB A:CYS19 3.4 71.5 1.0
N A:CYS19 3.4 75.6 1.0
CB A:HIS39 3.4 76.6 1.0
CB A:CYS16 3.4 90.0 1.0
CA A:CYS19 3.7 76.0 1.0
C A:ALA18 4.0 78.9 1.0
ND1 A:HIS33 4.1 65.0 1.0
CG A:HIS33 4.2 66.8 1.0
CD2 A:HIS39 4.3 81.3 1.0
NE2 A:HIS39 4.3 81.3 1.0
CB A:ALA18 4.3 81.2 1.0
CB A:ALA110 4.4 67.0 1.0
CA A:ALA18 4.5 80.5 1.0
O A:ALA18 4.6 78.2 1.0
N A:ALA18 4.7 78.9 1.0
CA A:CYS16 4.8 89.2 1.0
CA A:HIS39 4.9 71.4 1.0

Zinc binding site 3 out of 6 in 5rln

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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 Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.5
occ:1.00
 SG A:CYS5 2.2 99.4 1.0
SG A:CYS26 2.4 0.6 1.0
SG A:CYS8 2.7 1.0 1.0
SG A:CYS29 3.1 94.4 1.0
CB A:CYS29 3.1 0.1 1.0
CB A:CYS5 3.5 0.6 1.0
N A:CYS8 3.6 0.4 1.0
CB A:CYS26 3.7 0.7 1.0
CB A:CYS8 3.8 0.9 1.0
N A:CYS26 4.0 0.2 1.0
CB A:LEU7 4.0 0.6 1.0
CA A:CYS8 4.2 0.4 1.0
C A:LEU7 4.2 0.3 1.0
CA A:CYS26 4.4 0.6 1.0
CA A:CYS29 4.4 98.2 1.0
CA A:LEU7 4.4 0.8 1.0
N A:LEU7 4.5 0.8 1.0
N A:CYS29 4.5 0.4 1.0
CG A:LEU7 4.8 0.3 1.0
C A:CYS8 4.8 0.9 1.0
CA A:CYS5 4.9 0.9 1.0
CD1 A:LEU7 5.0 0.4 1.0

Zinc binding site 4 out of 6 in 5rln

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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 Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:55.3
occ:1.00
 NE2 B:HIS33 2.0 52.0 1.0
ND1 B:HIS39 2.2 51.5 1.0
SG B:CYS16 2.3 56.9 1.0
SG B:CYS19 2.4 54.7 1.0
CE1 B:HIS33 2.9 51.5 1.0
CD2 B:HIS33 3.1 50.8 1.0
CG B:HIS39 3.1 55.7 1.0
CE1 B:HIS39 3.2 52.0 1.0
CB B:HIS39 3.3 55.7 1.0
CB B:CYS16 3.4 56.5 1.0
N B:CYS19 3.4 55.4 1.0
CB B:CYS19 3.5 53.9 1.0
CA B:CYS19 3.8 53.7 1.0
C B:ALA18 4.0 54.5 1.0
ND1 B:HIS33 4.1 51.4 1.0
CG B:HIS33 4.2 51.6 1.0
CD2 B:HIS39 4.3 54.7 1.0
NE2 B:HIS39 4.3 52.7 1.0
CB B:ALA18 4.4 50.8 1.0
CB B:ALA110 4.5 46.4 1.0
CA B:ALA18 4.6 53.1 1.0
N B:ALA18 4.7 54.4 1.0
O B:ALA18 4.7 53.4 1.0
CA B:CYS16 4.7 57.6 1.0
CA B:HIS39 4.8 54.7 1.0
C B:CYS16 5.0 57.4 1.0

Zinc binding site 5 out of 6 in 5rln

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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 Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:73.7
occ:1.00
 SG B:CYS26 2.2 63.8 1.0
SG B:CYS5 2.3 64.9 1.0
SG B:CYS29 2.5 68.7 1.0
CB B:CYS8 2.9 84.4 1.0
CB B:CYS29 3.0 58.6 1.0
SG B:CYS8 3.0 88.0 1.0
CB B:CYS26 3.4 62.8 1.0
CB B:CYS5 3.5 70.6 1.0
N B:CYS8 3.9 77.2 1.0
N B:CYS26 3.9 63.6 1.0
CA B:CYS8 4.0 79.6 1.0
N B:CYS29 4.1 61.5 1.0
CA B:CYS29 4.1 59.2 1.0
CA B:CYS26 4.2 63.1 1.0
CB B:LEU7 4.5 72.0 1.0
N B:GLY99 4.5 80.4 1.0
C B:LEU7 4.6 76.1 1.0
CA B:GLY99 4.6 81.5 1.0
OG B:SER10 4.7 75.5 1.0
CB B:SER10 4.9 75.9 1.0
CA B:LEU7 4.9 74.0 1.0
N B:LEU7 4.9 73.0 1.0
C B:CYS26 4.9 64.5 1.0
CA B:CYS5 4.9 71.6 1.0
O B:CYS26 5.0 64.6 1.0
C B:GLY99 5.0 79.0 1.0

Zinc binding site 6 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:90.9
occ:1.00
 SG B:CYS50 2.2 88.9 1.0
ND1 B:HIS75 2.4 0.1 1.0
SG B:CYS55 2.5 0.6 1.0
SG B:CYS72 2.9 83.4 1.0
CB B:CYS55 3.1 0.6 1.0
CB B:CYS50 3.1 98.4 1.0
CG B:HIS75 3.3 0.4 1.0
CE1 B:HIS75 3.4 0.8 1.0
CB B:CYS72 3.5 78.7 1.0
CB B:HIS75 3.5 0.7 1.0
N B:CYS72 3.8 80.5 1.0
CB B:ALA52 4.0 0.3 1.0
CA B:CYS72 4.2 79.9 1.0
CG2 B:VAL57 4.5 89.3 1.0
CD2 B:HIS75 4.5 0.8 1.0
CA B:CYS50 4.5 95.8 1.0
NE2 B:HIS75 4.5 0.3 1.0
CA B:CYS55 4.5 0.2 1.0
N B:HIS75 4.6 92.9 1.0
CB B:VAL57 4.7 90.0 1.0
CA B:HIS75 4.7 96.6 1.0
C B:TYR71 4.9 81.3 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 04:06:32 2024

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