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Zinc in PDB 5rlo: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1454310449

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1454310449

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1454310449:
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 Z1454310449, PDB code: 5rlo 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) 81.35 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.065, 70.154, 85.301, 102.56, 96.34, 112.24
R / Rfree (%) 16.7 / 24.3

Other elements in 5rlo:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1454310449 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 Z1454310449 (pdb code 5rlo). 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 Z1454310449, PDB code: 5rlo:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlo

Go back to Zinc Binding Sites List in 5rlo
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1454310449


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 Z1454310449 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:75.0
occ:1.00
 SG A:CYS50 2.2 80.5 1.0
ND1 A:HIS75 2.4 73.2 1.0
SG A:CYS55 2.5 87.4 1.0
SG A:CYS72 2.9 81.9 1.0
CB A:CYS50 3.1 84.0 1.0
CB A:CYS72 3.2 82.0 1.0
CB A:CYS55 3.3 90.6 1.0
CG A:HIS75 3.4 71.5 1.0
CE1 A:HIS75 3.4 70.7 1.0
CB A:HIS75 3.6 70.7 1.0
N A:CYS72 3.6 77.1 1.0
CA A:CYS72 4.0 80.8 1.0
CG2 A:VAL57 4.4 79.3 1.0
CB A:ALA52 4.4 76.3 1.0
N A:HIS75 4.5 78.2 1.0
CB A:VAL57 4.5 80.0 1.0
CD2 A:HIS75 4.5 70.2 1.0
NE2 A:HIS75 4.5 69.6 1.0
CA A:CYS50 4.5 85.6 1.0
CA A:HIS75 4.7 73.0 1.0
CA A:CYS55 4.8 93.5 1.0
C A:CYS72 4.8 83.0 1.0
C A:TYR71 4.8 73.5 1.0

Zinc binding site 2 out of 6 in 5rlo

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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 Z1454310449


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 Z1454310449 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.8
occ:1.00
 NE2 A:HIS33 1.9 62.1 1.0
ND1 A:HIS39 2.1 84.8 1.0
SG A:CYS16 2.3 93.9 1.0
SG A:CYS19 2.5 73.6 1.0
CE1 A:HIS33 2.7 61.7 1.0
CG A:HIS39 3.1 85.4 1.0
CE1 A:HIS39 3.1 85.4 1.0
CD2 A:HIS33 3.1 65.6 1.0
CB A:HIS39 3.4 82.8 1.0
CB A:CYS16 3.4 92.0 1.0
CB A:CYS19 3.5 73.2 1.0
N A:CYS19 3.6 79.7 1.0
CA A:CYS19 3.9 76.3 1.0
ND1 A:HIS33 3.9 62.9 1.0
CG A:HIS33 4.1 66.3 1.0
CD2 A:HIS39 4.2 86.0 1.0
NE2 A:HIS39 4.2 85.8 1.0
C A:ALA18 4.3 86.0 1.0
CB A:ALA110 4.3 66.0 1.0
CB A:ALA18 4.5 85.9 1.0
CA A:CYS16 4.8 90.1 1.0
CA A:ALA18 4.8 85.4 1.0
CA A:HIS39 4.8 79.1 1.0
O A:ALA18 4.9 84.2 1.0
CE2 A:PHE106 4.9 77.5 1.0
N A:ALA18 4.9 85.0 1.0
CZ A:PHE106 5.0 77.5 1.0

Zinc binding site 3 out of 6 in 5rlo

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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 Z1454310449


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 Z1454310449 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.6
occ:1.00
 SG A:CYS29 2.2 93.3 1.0
SG A:CYS8 2.3 1.0 1.0
SG A:CYS26 2.4 0.9 1.0
SG A:CYS5 2.5 1.0 1.0
CB A:CYS29 3.1 94.5 1.0
CB A:CYS8 3.3 0.1 1.0
CB A:CYS5 3.5 0.6 1.0
CB A:CYS26 3.5 0.0 1.0
N A:CYS8 3.6 0.8 1.0
CA A:CYS8 3.9 0.6 1.0
N A:CYS26 4.2 0.7 1.0
CA A:CYS29 4.4 91.2 1.0
CA A:CYS26 4.4 0.4 1.0
N A:CYS29 4.4 96.4 1.0
CB A:LEU7 4.5 98.0 1.0
C A:CYS8 4.5 0.6 1.0
C A:LEU7 4.6 0.8 1.0
N A:ASN9 4.8 0.2 1.0
CB A:SER10 4.9 1.0 1.0
N A:LEU7 4.9 99.5 1.0
CA A:CYS5 4.9 99.5 1.0
CA A:LEU7 4.9 0.0 1.0
OG A:SER10 5.0 0.4 1.0
N A:SER10 5.0 0.7 1.0

Zinc binding site 4 out of 6 in 5rlo

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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 Z1454310449


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 Z1454310449 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:53.4
occ:1.00
 NE2 B:HIS33 2.0 50.0 1.0
ND1 B:HIS39 2.1 58.0 1.0
SG B:CYS16 2.2 59.8 1.0
SG B:CYS19 2.6 59.6 1.0
CE1 B:HIS33 2.8 53.1 1.0
CG B:HIS39 3.1 60.1 1.0
CD2 B:HIS33 3.1 49.2 1.0
CE1 B:HIS39 3.2 58.8 1.0
CB B:HIS39 3.3 59.9 1.0
CB B:CYS16 3.3 61.9 1.0
CB B:CYS19 3.4 59.8 1.0
N B:CYS19 3.5 60.9 1.0
CA B:CYS19 3.8 61.7 1.0
ND1 B:HIS33 4.0 52.8 1.0
CG B:HIS33 4.2 51.5 1.0
C B:ALA18 4.2 59.8 1.0
CD2 B:HIS39 4.2 61.8 1.0
NE2 B:HIS39 4.2 60.6 1.0
CB B:ALA18 4.4 56.9 1.0
CB B:ALA110 4.5 49.5 1.0
CA B:CYS16 4.7 61.5 1.0
CA B:ALA18 4.7 59.5 1.0
CA B:HIS39 4.8 59.8 1.0
N B:ALA18 4.8 61.4 1.0
O B:ALA18 4.8 61.3 1.0
C B:CYS16 5.0 63.0 1.0

Zinc binding site 5 out of 6 in 5rlo

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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 Z1454310449


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 Z1454310449 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:78.2
occ:1.00
 CB B:CYS8 2.4 93.0 1.0
SG B:CYS26 2.5 70.3 1.0
SG B:CYS5 2.5 77.1 1.0
SG B:CYS29 2.5 70.3 1.0
SG B:CYS8 3.0 1.0 1.0
CB B:CYS29 3.1 67.8 1.0
CB B:CYS5 3.5 80.2 1.0
CB B:CYS26 3.5 70.7 1.0
CA B:CYS8 3.6 92.2 1.0
N B:CYS8 3.6 94.6 1.0
N B:CYS26 4.0 68.3 1.0
N B:CYS29 4.1 69.0 1.0
CA B:CYS29 4.2 66.2 1.0
CA B:CYS26 4.3 70.3 1.0
C B:LEU7 4.4 90.6 1.0
CB B:LEU7 4.4 88.7 1.0
N B:GLY99 4.6 85.5 1.0
CB B:SER10 4.7 83.0 1.0
CA B:GLY99 4.7 86.2 1.0
C B:CYS8 4.7 93.9 1.0
OG B:SER10 4.7 77.9 1.0
CA B:LEU7 4.9 88.2 1.0
N B:ASN9 4.9 92.8 1.0
CA B:CYS5 4.9 78.5 1.0

Zinc binding site 6 out of 6 in 5rlo

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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 Z1454310449


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 Z1454310449 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:99.9
occ:1.00
 SG B:CYS50 2.2 95.9 1.0
SG B:CYS55 2.4 0.4 1.0
ND1 B:HIS75 2.5 98.8 1.0
SG B:CYS72 2.9 94.5 1.0
CB B:CYS50 3.0 0.3 1.0
CB B:CYS72 3.1 88.4 1.0
CB B:CYS55 3.3 0.4 1.0
CE1 B:HIS75 3.5 98.3 1.0
CG B:HIS75 3.5 97.6 1.0
N B:CYS72 3.6 87.0 1.0
CB B:HIS75 3.7 96.8 1.0
CA B:CYS72 4.0 90.7 1.0
CG2 B:VAL57 4.3 0.3 1.0
CB B:VAL57 4.4 0.6 1.0
CA B:CYS50 4.4 0.3 1.0
CB B:ALA52 4.5 0.5 1.0
N B:HIS75 4.6 96.5 1.0
NE2 B:HIS75 4.6 0.9 1.0
CD2 B:HIS75 4.7 99.4 1.0
CA B:CYS55 4.7 0.9 1.0
CA B:HIS75 4.8 97.3 1.0
C B:TYR71 4.8 84.7 1.0
C B:CYS72 4.8 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: Wed Dec 16 07:15:58 2020

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