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Zinc in PDB 5rmd: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z57614330

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z57614330

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z57614330:
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 Z57614330, PDB code: 5rmd 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) 81.65 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.479, 70.417, 85.584, 102.71, 95.94, 112.61
R / Rfree (%) 21.7 / 26.1

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 Z57614330 (pdb code 5rmd). 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 Z57614330, PDB code: 5rmd:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmd

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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 Z57614330


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 Z57614330 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:47.6
occ:1.00
 SG A:CYS55 2.2 49.6 1.0
SG A:CYS50 2.2 42.7 1.0
ND1 A:HIS75 2.3 44.8 1.0
SG A:CYS72 2.5 49.4 1.0
CE1 A:HIS75 3.2 45.3 1.0
CB A:CYS50 3.2 49.8 1.0
CB A:CYS55 3.3 48.6 1.0
CG A:HIS75 3.3 42.9 1.0
CB A:CYS72 3.5 47.7 1.0
CB A:HIS75 3.6 39.5 1.0
N A:CYS72 3.8 44.5 1.0
CA A:CYS72 4.2 46.2 1.0
CB A:ALA52 4.3 47.3 1.0
NE2 A:HIS75 4.3 41.5 1.0
CD2 A:HIS75 4.4 45.8 1.0
CG2 A:VAL57 4.5 50.3 1.0
N A:HIS75 4.6 44.6 1.0
CA A:CYS50 4.6 46.4 1.0
CA A:CYS55 4.6 54.3 1.0
CA A:HIS75 4.7 39.7 1.0
CB A:VAL57 4.7 50.0 1.0
C A:CYS72 4.9 51.1 1.0
C A:TYR71 5.0 39.0 1.0
CB A:SER74 5.0 51.1 1.0

Zinc binding site 2 out of 6 in 5rmd

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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 Z57614330


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 Z57614330 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:43.3
occ:1.00
 NE2 A:HIS33 2.0 26.8 1.0
ND1 A:HIS39 2.1 51.1 1.0
SG A:CYS16 2.2 57.0 1.0
SG A:CYS19 2.4 42.3 1.0
CE1 A:HIS33 2.9 35.6 1.0
CE1 A:HIS39 3.0 55.4 1.0
CD2 A:HIS33 3.1 34.8 1.0
CG A:HIS39 3.1 54.0 1.0
N A:CYS19 3.1 44.0 1.0
CB A:CYS16 3.3 56.0 1.0
CB A:HIS39 3.4 51.6 1.0
CB A:CYS19 3.4 34.8 1.0
CA A:CYS19 3.6 41.7 1.0
ND1 A:HIS33 4.0 40.0 1.0
C A:ALA18 4.1 48.6 1.0
CB A:ALA18 4.1 51.0 1.0
NE2 A:HIS39 4.1 54.4 1.0
CD2 A:HIS39 4.2 59.6 1.0
CG A:HIS33 4.2 36.6 1.0
CA A:ALA18 4.5 49.9 1.0
CB A:ALA110 4.5 51.0 1.0
N A:ALA18 4.6 43.5 1.0
CA A:CYS16 4.6 53.1 1.0
CA A:HIS39 4.9 50.3 1.0
CE2 A:PHE106 4.9 49.3 1.0
C A:CYS16 5.0 46.7 1.0

Zinc binding site 3 out of 6 in 5rmd

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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 Z57614330


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 Z57614330 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:62.5
occ:1.00
 SG A:CYS5 2.3 60.3 1.0
SG A:CYS29 2.3 57.9 1.0
SG A:CYS8 2.5 74.6 1.0
SG A:CYS26 2.6 70.0 1.0
CB A:CYS29 3.1 61.1 1.0
CB A:CYS5 3.1 64.0 1.0
CB A:CYS26 3.1 63.2 1.0
CB A:CYS8 3.5 75.1 1.0
N A:CYS26 3.7 60.4 1.0
N A:CYS8 3.8 76.8 1.0
CA A:CYS26 4.0 65.9 1.0
CA A:CYS8 4.2 76.9 1.0
CA A:CYS29 4.3 61.8 1.0
N A:CYS29 4.4 64.2 1.0
CB A:LEU7 4.5 76.3 1.0
CA A:CYS5 4.6 67.4 1.0
CB A:SER10 4.6 65.3 1.0
C A:CYS26 4.7 71.8 1.0
O A:CYS26 4.7 73.0 1.0
C A:CYS8 4.8 72.2 1.0
C A:LEU7 4.8 71.2 1.0
N A:ASN9 4.9 73.0 1.0
C A:LEU25 4.9 59.8 1.0
N A:LEU7 4.9 63.4 1.0
CA A:LEU7 5.0 73.3 1.0
OG A:SER10 5.0 58.8 1.0

Zinc binding site 4 out of 6 in 5rmd

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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 Z57614330


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 Z57614330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:42.6
occ:1.00
 NE2 B:HIS33 2.0 31.3 1.0
SG B:CYS16 2.1 42.2 1.0
ND1 B:HIS39 2.2 45.2 1.0
SG B:CYS19 2.5 44.9 1.0
CD2 B:HIS33 2.9 31.7 1.0
CE1 B:HIS33 3.0 33.8 1.0
CG B:HIS39 3.1 48.2 1.0
CE1 B:HIS39 3.2 44.2 1.0
CB B:CYS16 3.3 56.8 1.0
CB B:HIS39 3.4 44.5 1.0
N B:CYS19 3.4 52.4 1.0
CB B:CYS19 3.4 39.3 1.0
CA B:CYS19 3.8 46.1 1.0
CG B:HIS33 4.1 31.4 1.0
ND1 B:HIS33 4.1 30.9 1.0
CD2 B:HIS39 4.2 46.7 1.0
NE2 B:HIS39 4.2 44.6 1.0
C B:ALA18 4.3 50.4 1.0
CB B:ALA18 4.4 47.8 1.0
CB B:ALA110 4.4 38.3 1.0
CA B:CYS16 4.6 57.9 1.0
CA B:ALA18 4.7 52.3 1.0
N B:ALA18 4.8 52.2 1.0
CA B:HIS39 4.8 45.8 1.0
C B:CYS16 4.9 54.9 1.0
CE2 B:PHE106 5.0 38.5 1.0
O B:CYS16 5.0 67.9 1.0

Zinc binding site 5 out of 6 in 5rmd

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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 Z57614330


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 Z57614330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:74.3
occ:1.00
 SG B:CYS26 2.3 61.2 1.0
SG B:CYS5 2.3 67.6 1.0
SG B:CYS29 2.3 61.4 1.0
CB B:CYS29 2.8 60.1 1.0
CB B:CYS26 2.8 62.2 1.0
CB B:CYS8 3.0 85.5 1.0
SG B:CYS8 3.0 73.2 1.0
CB B:CYS5 3.4 78.5 1.0
N B:CYS26 3.5 62.9 1.0
CA B:CYS26 3.7 57.4 1.0
N B:CYS8 4.0 84.6 1.0
CA B:CYS29 4.0 58.4 1.0
N B:CYS29 4.0 61.1 1.0
CA B:CYS8 4.1 88.4 1.0
CA B:GLY99 4.2 60.5 1.0
N B:GLY99 4.3 63.4 1.0
C B:CYS26 4.3 54.0 1.0
O B:CYS26 4.4 39.2 1.0
CB B:LEU7 4.7 94.3 1.0
C B:LEU25 4.7 65.6 1.0
CA B:CYS5 4.8 79.1 1.0
C B:GLY99 4.8 56.2 1.0
CB B:SER10 4.9 83.2 1.0
C B:LEU7 4.9 79.9 1.0
OG B:SER100 4.9 54.5 1.0

Zinc binding site 6 out of 6 in 5rmd

Go back to Zinc Binding Sites List in 5rmd
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z57614330


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 Z57614330 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:87.2
occ:1.00
 SG B:CYS50 2.2 62.9 1.0
SG B:CYS55 2.2 98.3 1.0
ND1 B:HIS75 2.5 95.1 1.0
SG B:CYS72 2.8 73.2 1.0
CB B:CYS55 3.2 0.3 1.0
CB B:CYS50 3.2 73.9 1.0
CG B:HIS75 3.4 93.0 1.0
CB B:CYS72 3.5 74.5 1.0
CE1 B:HIS75 3.5 97.8 1.0
CB B:HIS75 3.5 90.8 1.0
N B:CYS72 3.9 68.1 1.0
CB B:ALA52 4.1 98.8 1.0
CA B:CYS72 4.3 73.2 1.0
N B:HIS75 4.5 77.2 1.0
CG2 B:VAL57 4.5 69.9 1.0
CA B:CYS55 4.6 0.2 1.0
CD2 B:HIS75 4.6 95.8 1.0
CA B:CYS50 4.6 76.0 1.0
CA B:HIS75 4.6 85.2 1.0
NE2 B:HIS75 4.6 96.1 1.0
CB B:VAL57 4.7 77.9 1.0
C B:TYR71 5.0 70.8 1.0
C B:CYS72 5.0 77.6 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 04:23:18 2024

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