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Zinc in PDB 5rm0: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719:
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 Z1492796719, PDB code: 5rm0 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) 81.27 / 1.91
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.095, 70.190, 85.226, 102.66, 96.15, 112.43
R / Rfree (%) 16.8 / 23.9

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 Z1492796719 (pdb code 5rm0). 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 Z1492796719, PDB code: 5rm0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm0

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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 Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:72.2
occ:1.00
 SG A:CYS50 2.3 70.9 1.0
ND1 A:HIS75 2.3 65.3 1.0
SG A:CYS55 2.3 81.7 1.0
SG A:CYS72 2.8 70.0 1.0
CB A:CYS50 3.2 74.4 1.0
CB A:CYS55 3.3 81.5 1.0
CE1 A:HIS75 3.3 65.7 1.0
CG A:HIS75 3.3 64.7 1.0
CB A:CYS72 3.4 73.6 1.0
CB A:HIS75 3.6 64.5 1.0
N A:CYS72 3.8 68.6 1.0
CA A:CYS72 4.2 71.9 1.0
CB A:ALA52 4.3 69.7 1.0
NE2 A:HIS75 4.4 63.4 1.0
CG2 A:VAL57 4.4 75.7 1.0
CD2 A:HIS75 4.5 64.0 1.0
N A:HIS75 4.5 69.5 1.0
CA A:CYS50 4.6 72.8 1.0
CB A:VAL57 4.6 75.1 1.0
CA A:CYS55 4.7 84.4 1.0
CA A:HIS75 4.7 66.9 1.0
C A:TYR71 4.9 64.1 1.0
C A:CYS72 5.0 76.0 1.0

Zinc binding site 2 out of 6 in 5rm0

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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 Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:69.4
occ:1.00
 ND1 A:HIS39 2.0 76.4 1.0
NE2 A:HIS33 2.0 59.7 1.0
SG A:CYS16 2.4 79.6 1.0
SG A:CYS19 2.5 68.5 1.0
CE1 A:HIS33 3.0 60.8 1.0
CE1 A:HIS39 3.0 77.1 1.0
CG A:HIS39 3.0 77.9 1.0
CD2 A:HIS33 3.0 62.9 1.0
CB A:HIS39 3.3 73.2 1.0
CB A:CYS19 3.4 67.1 1.0
N A:CYS19 3.4 71.0 1.0
CB A:CYS16 3.5 78.0 1.0
CA A:CYS19 3.8 70.1 1.0
C A:ALA18 4.1 77.7 1.0
ND1 A:HIS33 4.1 63.3 1.0
NE2 A:HIS39 4.2 78.3 1.0
CG A:HIS33 4.2 66.1 1.0
CD2 A:HIS39 4.2 78.6 1.0
CB A:ALA18 4.4 77.2 1.0
CB A:ALA110 4.4 63.0 1.0
CA A:ALA18 4.6 77.2 1.0
N A:ALA18 4.8 75.5 1.0
O A:ALA18 4.8 80.1 1.0
CA A:CYS16 4.8 78.3 1.0
CA A:HIS39 4.8 74.0 1.0
CE2 A:PHE106 5.0 75.7 1.0

Zinc binding site 3 out of 6 in 5rm0

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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 Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.2
occ:1.00
 SG A:CYS26 2.2 92.4 1.0
SG A:CYS5 2.3 93.5 1.0
SG A:CYS8 2.4 0.7 1.0
SG A:CYS29 2.5 100.0 1.0
CB A:CYS29 3.3 96.0 1.0
CB A:CYS5 3.4 91.1 1.0
CB A:CYS8 3.4 0.5 1.0
CB A:CYS26 3.5 93.5 1.0
N A:CYS8 3.6 0.9 1.0
CA A:CYS8 4.0 0.3 1.0
N A:CYS26 4.0 93.3 1.0
N A:CYS29 4.3 95.3 1.0
CA A:CYS26 4.3 97.2 1.0
CB A:LEU7 4.3 0.6 1.0
CA A:CYS29 4.4 90.7 1.0
C A:LEU7 4.5 0.5 1.0
C A:CYS8 4.6 0.1 1.0
CA A:LEU7 4.8 0.9 1.0
CB A:SER10 4.8 0.0 1.0
N A:LEU7 4.8 0.1 1.0
CA A:CYS5 4.8 92.3 1.0
N A:ASN9 4.8 0.7 1.0
OG A:SER10 4.8 0.4 1.0
O A:CYS26 4.9 0.4 1.0
C A:CYS26 5.0 0.1 1.0

Zinc binding site 4 out of 6 in 5rm0

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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 Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:52.4
occ:1.00
 NE2 B:HIS33 2.1 51.9 1.0
ND1 B:HIS39 2.2 54.5 1.0
SG B:CYS16 2.2 58.1 1.0
SG B:CYS19 2.6 57.0 1.0
CD2 B:HIS33 3.0 50.6 1.0
CG B:HIS39 3.1 54.9 1.0
CE1 B:HIS33 3.1 52.0 1.0
CE1 B:HIS39 3.2 55.6 1.0
CB B:CYS16 3.3 61.8 1.0
CB B:HIS39 3.3 53.9 1.0
CB B:CYS19 3.4 55.4 1.0
N B:CYS19 3.4 57.3 1.0
CA B:CYS19 3.8 56.5 1.0
C B:ALA18 4.1 56.0 1.0
CG B:HIS33 4.2 52.0 1.0
ND1 B:HIS33 4.2 51.3 1.0
CD2 B:HIS39 4.3 56.1 1.0
NE2 B:HIS39 4.3 57.1 1.0
CB B:ALA18 4.3 52.9 1.0
CA B:ALA18 4.6 55.0 1.0
CA B:CYS16 4.6 62.4 1.0
N B:ALA18 4.7 56.8 1.0
CB B:ALA110 4.7 50.8 1.0
CA B:HIS39 4.8 54.1 1.0
O B:ALA18 4.9 54.9 1.0
C B:CYS16 4.9 64.3 1.0

Zinc binding site 5 out of 6 in 5rm0

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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 Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:88.7
occ:1.00
 SG B:CYS26 2.2 80.8 1.0
SG B:CYS5 2.3 74.3 1.0
SG B:CYS29 2.4 83.4 1.0
CB B:CYS8 2.8 90.0 1.0
CB B:CYS29 3.1 70.8 1.0
SG B:CYS8 3.2 96.1 1.0
CB B:CYS5 3.4 81.9 1.0
CB B:CYS26 3.5 81.5 1.0
N B:CYS8 3.7 89.7 1.0
CA B:CYS8 3.9 90.3 1.0
N B:CYS26 3.9 76.3 1.0
N B:CYS29 4.1 70.3 1.0
CA B:CYS29 4.2 67.5 1.0
CA B:CYS26 4.2 80.5 1.0
CB B:LEU7 4.4 85.8 1.0
C B:LEU7 4.6 86.4 1.0
N B:GLY99 4.8 79.7 1.0
CB B:SER10 4.8 82.3 1.0
O B:CYS26 4.8 82.4 1.0
OG B:SER10 4.8 79.1 1.0
CA B:CYS5 4.8 79.9 1.0
C B:CYS26 4.8 81.5 1.0
C B:CYS8 4.9 90.5 1.0
CA B:LEU7 4.9 85.4 1.0
N B:LEU7 4.9 82.8 1.0
CA B:GLY99 4.9 78.5 1.0

Zinc binding site 6 out of 6 in 5rm0

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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 Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:86.5
occ:1.00
 SG B:CYS50 2.2 87.0 1.0
SG B:CYS55 2.3 0.1 1.0
ND1 B:HIS75 2.4 88.3 1.0
SG B:CYS72 2.9 84.9 1.0
CB B:CYS50 3.1 88.8 1.0
CB B:CYS55 3.2 0.7 1.0
CE1 B:HIS75 3.3 90.9 1.0
CG B:HIS75 3.4 87.6 1.0
CB B:CYS72 3.5 79.8 1.0
CB B:HIS75 3.6 85.1 1.0
N B:CYS72 3.8 80.1 1.0
CB B:ALA52 4.2 1.0 1.0
CA B:CYS72 4.3 80.3 1.0
CG2 B:VAL57 4.4 91.2 1.0
NE2 B:HIS75 4.5 92.3 1.0
CD2 B:HIS75 4.5 90.2 1.0
CA B:CYS50 4.5 90.0 1.0
N B:HIS75 4.6 85.0 1.0
CB B:VAL57 4.6 91.7 1.0
CA B:CYS55 4.6 0.1 1.0
CA B:HIS75 4.8 86.2 1.0
C B:TYR71 4.9 78.0 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 04:11:58 2024

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