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Zinc in PDB 5rl6: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z198195770

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z198195770

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z198195770:
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 Z198195770, PDB code: 5rl6 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) 81.59 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.363, 70.300, 85.934, 103.23, 96.43, 112.23
R / Rfree (%) 17.8 / 25

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 Z198195770 (pdb code 5rl6). 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 Z198195770, PDB code: 5rl6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rl6

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:53.1
occ:1.00
 ND1 A:HIS75 2.2 50.9 1.0
SG A:CYS50 2.3 51.6 1.0
SG A:CYS55 2.4 58.9 1.0
SG A:CYS72 2.5 48.3 1.0
CG A:HIS75 3.2 48.9 1.0
CE1 A:HIS75 3.2 49.7 1.0
CB A:CYS50 3.3 55.1 1.0
CB A:CYS55 3.3 58.9 1.0
CB A:CYS72 3.4 54.0 1.0
CB A:HIS75 3.4 48.0 1.0
N A:CYS72 3.8 52.4 1.0
CA A:CYS72 4.2 54.4 1.0
CB A:ALA52 4.2 48.8 1.0
CD2 A:HIS75 4.4 48.0 1.0
NE2 A:HIS75 4.4 48.1 1.0
N A:HIS75 4.4 51.4 1.0
CG2 A:VAL57 4.5 59.5 1.0
CA A:HIS75 4.6 50.0 1.0
CA A:CYS50 4.7 56.4 1.0
CB A:VAL57 4.7 61.5 1.0
CA A:CYS55 4.7 62.7 1.0
C A:CYS72 4.8 56.0 1.0
O A:CYS72 4.9 56.7 1.0
C A:TYR71 4.9 52.0 1.0
CB A:SER74 4.9 55.6 1.0

Zinc binding site 2 out of 6 in 5rl6

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:62.7
occ:1.00
 ND1 A:HIS39 2.0 62.6 1.0
NE2 A:HIS33 2.1 63.0 1.0
SG A:CYS19 2.2 62.5 1.0
SG A:CYS16 2.4 69.9 1.0
CE1 A:HIS39 3.0 61.0 1.0
CD2 A:HIS33 3.0 63.6 1.0
CG A:HIS39 3.1 62.7 1.0
CE1 A:HIS33 3.2 63.0 1.0
CB A:CYS16 3.2 72.4 1.0
N A:CYS19 3.4 58.8 1.0
CB A:CYS19 3.4 60.1 1.0
CB A:HIS39 3.5 62.4 1.0
CA A:CYS19 3.7 59.8 1.0
C A:ALA18 4.1 60.2 1.0
NE2 A:HIS39 4.1 63.6 1.0
CG A:HIS33 4.2 64.0 1.0
CD2 A:HIS39 4.2 62.9 1.0
ND1 A:HIS33 4.3 63.8 1.0
CB A:ALA110 4.4 58.1 1.0
CB A:ALA18 4.4 60.2 1.0
CA A:ALA18 4.6 62.0 1.0
CA A:CYS16 4.7 72.8 1.0
N A:ALA18 4.7 62.8 1.0
CE2 A:PHE106 4.9 63.7 1.0
O A:ALA18 4.9 62.4 1.0
CA A:HIS39 5.0 61.7 1.0
CZ A:PHE106 5.0 63.0 1.0

Zinc binding site 3 out of 6 in 5rl6

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.8
occ:1.00
 SG A:CYS29 2.3 84.7 1.0
SG A:CYS8 2.3 88.3 1.0
SG A:CYS5 2.5 70.2 1.0
SG A:CYS26 2.6 87.5 1.0
CB A:CYS26 3.1 89.8 1.0
CB A:CYS8 3.2 92.2 1.0
CB A:CYS29 3.2 82.4 1.0
CB A:CYS5 3.6 78.5 1.0
N A:CYS8 3.6 94.5 1.0
N A:CYS26 3.8 88.8 1.0
CA A:CYS8 3.9 94.9 1.0
CA A:CYS26 4.0 89.0 1.0
N A:CYS29 4.2 81.3 1.0
CA A:CYS29 4.4 81.3 1.0
CB A:LEU7 4.4 95.3 1.0
C A:LEU7 4.5 93.4 1.0
C A:CYS8 4.6 0.8 1.0
OG A:SER10 4.7 85.6 1.0
N A:ASN9 4.8 0.7 1.0
CB A:SER10 4.8 93.6 1.0
C A:CYS26 4.8 92.3 1.0
CA A:LEU7 4.8 90.3 1.0
CA A:CYS5 5.0 80.8 1.0
N A:SER10 5.0 0.3 1.0
N A:LEU7 5.0 88.4 1.0
O A:CYS26 5.0 93.5 1.0

Zinc binding site 4 out of 6 in 5rl6

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:48.0
occ:1.00
 NE2 B:HIS33 2.0 49.2 1.0
ND1 B:HIS39 2.0 48.7 1.0
SG B:CYS16 2.2 52.7 1.0
SG B:CYS19 2.4 50.5 1.0
CD2 B:HIS33 2.9 47.6 1.0
CE1 B:HIS39 3.0 49.6 1.0
CG B:HIS39 3.1 49.7 1.0
CE1 B:HIS33 3.1 47.8 1.0
CB B:CYS16 3.3 52.6 1.0
CB B:CYS19 3.4 51.6 1.0
CB B:HIS39 3.4 50.0 1.0
N B:CYS19 3.5 53.4 1.0
CA B:CYS19 3.8 52.8 1.0
CG B:HIS33 4.1 47.9 1.0
NE2 B:HIS39 4.2 50.7 1.0
CD2 B:HIS39 4.2 50.2 1.0
C B:ALA18 4.2 53.1 1.0
ND1 B:HIS33 4.2 46.6 1.0
CB B:ALA18 4.5 51.7 1.0
CB B:ALA110 4.6 47.5 1.0
CA B:CYS16 4.7 51.5 1.0
CA B:ALA18 4.7 52.3 1.0
N B:ALA18 4.8 52.3 1.0
CA B:HIS39 4.9 50.6 1.0
O B:ALA18 4.9 55.1 1.0

Zinc binding site 5 out of 6 in 5rl6

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:62.0
occ:1.00
 SG B:CYS29 2.3 59.7 1.0
SG B:CYS5 2.3 57.6 1.0
SG B:CYS26 2.4 57.4 1.0
CB B:CYS8 2.7 77.8 1.0
SG B:CYS8 2.9 91.7 1.0
CB B:CYS29 3.0 53.3 1.0
CB B:CYS5 3.4 61.8 1.0
CB B:CYS26 3.6 54.9 1.0
N B:CYS8 3.7 77.9 1.0
CA B:CYS8 3.9 76.0 1.0
N B:CYS26 3.9 55.2 1.0
N B:CYS29 4.0 52.9 1.0
CA B:CYS29 4.1 51.0 1.0
CA B:CYS26 4.3 53.5 1.0
CB B:LEU7 4.5 72.6 1.0
C B:LEU7 4.6 75.7 1.0
N B:GLY99 4.6 83.4 1.0
CA B:GLY99 4.7 86.9 1.0
OG B:SER10 4.8 63.9 1.0
CA B:CYS5 4.8 62.9 1.0
CB B:SER10 4.9 65.1 1.0
C B:CYS8 4.9 73.7 1.0
CA B:LEU7 4.9 70.8 1.0
N B:LEU7 4.9 68.9 1.0
C B:GLY99 5.0 87.6 1.0

Zinc binding site 6 out of 6 in 5rl6

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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 Z198195770


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 Z198195770 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:63.7
occ:1.00
 ND1 B:HIS75 2.2 73.9 1.0
SG B:CYS50 2.3 64.8 1.0
SG B:CYS55 2.4 72.1 1.0
SG B:CYS72 2.5 62.5 1.0
CG B:HIS75 3.1 73.8 1.0
CE1 B:HIS75 3.2 72.0 1.0
CB B:CYS50 3.2 69.9 1.0
CB B:CYS55 3.3 76.4 1.0
CB B:HIS75 3.4 70.3 1.0
CB B:CYS72 3.4 64.0 1.0
N B:CYS72 3.8 64.3 1.0
CB B:ALA52 4.0 73.0 1.0
CA B:CYS72 4.1 64.6 1.0
N B:HIS75 4.3 70.6 1.0
CD2 B:HIS75 4.3 73.2 1.0
NE2 B:HIS75 4.3 72.7 1.0
CA B:HIS75 4.5 71.4 1.0
CG2 B:VAL57 4.5 58.0 1.0
CA B:CYS50 4.7 70.4 1.0
CA B:CYS55 4.7 76.8 1.0
CB B:VAL57 4.7 62.0 1.0
C B:CYS72 4.8 68.0 1.0
CB B:SER74 4.9 64.5 1.0
O B:CYS72 4.9 66.2 1.0
C B:TYR71 4.9 63.3 1.0
C B:SER74 4.9 72.5 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: Mon Oct 28 03:54:06 2024

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