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Zinc in PDB 5rm5: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900:
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 Z373768900, PDB code: 5rm5 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) 81.15 / 2.06
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.094, 70.181, 85.187, 103.00, 95.97, 112.29
R / Rfree (%) 20.6 / 26.2

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 Z373768900 (pdb code 5rm5). 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 Z373768900, PDB code: 5rm5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm5

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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 Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:51.2
occ:1.00
 ND1 A:HIS75 2.2 45.1 1.0
SG A:CYS55 2.2 55.4 1.0
SG A:CYS50 2.2 51.3 1.0
SG A:CYS72 2.5 48.4 1.0
CE1 A:HIS75 3.1 45.0 1.0
CG A:HIS75 3.1 44.0 1.0
CB A:CYS55 3.2 51.2 1.0
CB A:CYS50 3.2 55.3 1.0
CB A:CYS72 3.3 51.3 1.0
CB A:HIS75 3.4 46.2 1.0
N A:CYS72 3.8 51.4 1.0
CB A:ALA52 4.1 55.6 1.0
CA A:CYS72 4.1 52.4 1.0
NE2 A:HIS75 4.2 43.4 1.0
CD2 A:HIS75 4.3 42.8 1.0
CG2 A:VAL57 4.5 64.5 1.0
N A:HIS75 4.6 50.6 1.0
CA A:CYS55 4.6 56.2 1.0
CA A:HIS75 4.6 45.8 1.0
CA A:CYS50 4.7 54.7 1.0
CB A:VAL57 4.7 62.2 1.0
C A:CYS72 4.9 60.6 1.0
CB A:SER74 4.9 57.8 1.0
C A:TYR71 5.0 47.1 1.0

Zinc binding site 2 out of 6 in 5rm5

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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 Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:56.3
occ:1.00
 NE2 A:HIS33 1.8 32.6 1.0
ND1 A:HIS39 2.0 62.7 1.0
SG A:CYS16 2.1 82.6 1.0
SG A:CYS19 2.4 53.9 1.0
CE1 A:HIS33 2.8 40.4 1.0
CD2 A:HIS33 2.9 40.5 1.0
CE1 A:HIS39 3.0 69.5 1.0
CG A:HIS39 3.0 72.0 1.0
N A:CYS19 3.2 52.2 1.0
CB A:CYS16 3.2 76.0 1.0
CB A:HIS39 3.4 66.4 1.0
CB A:CYS19 3.6 40.3 1.0
CA A:CYS19 3.8 49.4 1.0
ND1 A:HIS33 3.9 43.0 1.0
CG A:HIS33 4.0 41.9 1.0
C A:ALA18 4.1 64.8 1.0
NE2 A:HIS39 4.1 68.5 1.0
CB A:ALA18 4.2 74.2 1.0
CD2 A:HIS39 4.2 76.7 1.0
CB A:ALA110 4.4 62.9 1.0
CA A:ALA18 4.5 70.2 1.0
CA A:CYS16 4.6 70.5 1.0
N A:ALA18 4.7 62.7 1.0
CE2 A:PHE106 4.8 48.1 1.0
CA A:HIS39 4.8 61.6 1.0
CZ A:PHE106 5.0 49.0 1.0

Zinc binding site 3 out of 6 in 5rm5

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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 Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:84.4
occ:1.00
 SG A:CYS5 2.1 87.1 1.0
SG A:CYS8 2.3 0.8 1.0
SG A:CYS29 2.5 74.4 1.0
SG A:CYS26 2.6 82.2 1.0
CB A:CYS26 3.1 78.0 1.0
CB A:CYS29 3.1 84.0 1.0
CB A:CYS5 3.3 91.0 1.0
CB A:CYS8 3.6 0.7 1.0
N A:CYS8 3.7 0.3 1.0
N A:CYS26 3.8 73.3 1.0
CA A:CYS26 3.9 80.1 1.0
CA A:CYS8 4.1 0.1 1.0
CB A:LEU7 4.3 96.0 1.0
CA A:CYS29 4.4 81.1 1.0
N A:CYS29 4.5 76.3 1.0
C A:CYS8 4.5 94.4 1.0
CA A:CYS5 4.6 91.9 1.0
C A:LEU7 4.7 94.0 1.0
C A:CYS26 4.7 90.4 1.0
O A:CYS26 4.7 88.3 1.0
N A:ASN9 4.7 0.7 1.0
CB A:SER10 4.7 86.3 1.0
N A:LEU7 4.8 82.5 1.0
O A:CYS5 4.8 84.4 1.0
CA A:LEU7 4.8 91.7 1.0
C A:CYS5 4.9 94.1 1.0
C A:LEU25 5.0 76.0 1.0

Zinc binding site 4 out of 6 in 5rm5

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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 Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:39.0
occ:1.00
 NE2 B:HIS33 2.0 34.8 1.0
ND1 B:HIS39 2.1 51.1 1.0
SG B:CYS16 2.1 43.8 1.0
SG B:CYS19 2.3 40.9 1.0
CD2 B:HIS33 3.0 35.3 1.0
CE1 B:HIS33 3.0 40.4 1.0
CG B:HIS39 3.0 56.0 1.0
CE1 B:HIS39 3.1 53.4 1.0
CB B:CYS16 3.3 45.9 1.0
CB B:HIS39 3.3 47.7 1.0
CB B:CYS19 3.4 43.3 1.0
N B:CYS19 3.4 51.4 1.0
CA B:CYS19 3.8 45.4 1.0
ND1 B:HIS33 4.1 35.5 1.0
CG B:HIS33 4.1 38.0 1.0
NE2 B:HIS39 4.2 52.8 1.0
CD2 B:HIS39 4.2 52.2 1.0
C B:ALA18 4.3 52.3 1.0
CB B:ALA110 4.5 40.0 1.0
CB B:ALA18 4.6 42.1 1.0
CA B:CYS16 4.7 45.5 1.0
CA B:ALA18 4.8 47.4 1.0
CA B:HIS39 4.8 47.1 1.0
N B:ALA18 4.9 48.2 1.0
CE2 B:PHE106 5.0 39.5 1.0

Zinc binding site 5 out of 6 in 5rm5

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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 Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:58.7
occ:1.00
 SG B:CYS26 2.1 63.6 1.0
SG B:CYS29 2.2 54.1 1.0
SG B:CYS5 2.3 62.2 1.0
CB B:CYS29 2.9 49.5 1.0
CB B:CYS8 3.0 74.4 1.0
SG B:CYS8 3.2 80.4 1.0
CB B:CYS26 3.4 61.8 1.0
CB B:CYS5 3.4 68.5 1.0
N B:CYS26 3.8 65.6 1.0
N B:CYS8 3.8 77.7 1.0
CA B:CYS8 4.0 79.3 1.0
N B:CYS29 4.1 51.4 1.0
CA B:CYS29 4.1 49.2 1.0
CA B:CYS26 4.1 68.4 1.0
CB B:LEU7 4.5 82.1 1.0
C B:LEU7 4.6 79.2 1.0
O B:CYS26 4.7 66.9 1.0
CB B:SER10 4.7 64.9 1.0
N B:GLY99 4.7 66.0 1.0
OG B:SER10 4.7 69.7 1.0
C B:CYS26 4.7 69.8 1.0
CA B:GLY99 4.8 62.2 1.0
CA B:CYS5 4.8 71.8 1.0
CA B:LEU7 4.9 80.0 1.0
C B:LEU25 4.9 63.4 1.0
N B:LEU7 5.0 64.7 1.0

Zinc binding site 6 out of 6 in 5rm5

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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 Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:73.0
occ:1.00
 SG B:CYS50 2.2 67.9 1.0
SG B:CYS55 2.3 77.5 1.0
ND1 B:HIS75 2.4 86.6 1.0
SG B:CYS72 2.7 61.7 1.0
CB B:CYS55 3.0 86.8 1.0
CB B:CYS50 3.1 66.7 1.0
CG B:HIS75 3.3 83.1 1.0
CB B:HIS75 3.4 75.4 1.0
CE1 B:HIS75 3.5 86.7 1.0
CB B:CYS72 3.6 59.2 1.0
N B:CYS72 3.9 56.6 1.0
CB B:ALA52 4.0 85.7 1.0
CG2 B:VAL57 4.3 70.8 1.0
CA B:CYS72 4.3 61.0 1.0
CD2 B:HIS75 4.5 87.5 1.0
N B:HIS75 4.5 62.0 1.0
CA B:CYS50 4.5 72.2 1.0
CA B:CYS55 4.5 87.9 1.0
NE2 B:HIS75 4.5 84.9 1.0
CA B:HIS75 4.6 72.2 1.0
CB B:VAL57 4.7 75.3 1.0
N B:ALA52 5.0 85.5 1.0
C B:CYS50 5.0 82.9 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 04:17:42 2024

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