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Zinc in PDB 5rm4: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1639162606

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1639162606

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1639162606:
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 Z1639162606, PDB code: 5rm4 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) 81.64 / 2.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.219, 70.367, 85.533, 102.41, 96.27, 112.45
R / Rfree (%) 16.8 / 25.3

Other elements in 5rm4:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1639162606 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 Z1639162606 (pdb code 5rm4). 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 Z1639162606, PDB code: 5rm4:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm4

Go back to Zinc Binding Sites List in 5rm4
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1639162606


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 Z1639162606 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:31.4
occ:1.00
 NE2 B:HIS33 2.0 31.0 1.0
SG B:CYS16 2.3 41.5 1.0
SG B:CYS19 2.5 29.9 1.0
ND1 B:HIS39 2.8 41.6 1.0
CD2 B:HIS33 3.0 33.4 1.0
CE1 B:HIS33 3.0 32.9 1.0
CG B:HIS39 3.2 44.7 1.0
CB B:HIS39 3.3 46.5 1.0
CB B:CYS16 3.3 43.6 1.0
CB B:CYS19 3.4 30.8 1.0
N B:CYS19 3.4 36.3 1.0
CE1 B:HIS39 3.7 39.0 1.0
CA B:CYS19 3.8 33.6 1.0
ND1 B:HIS33 4.1 34.2 1.0
CD2 B:HIS39 4.1 42.9 1.0
CG B:HIS33 4.1 36.2 1.0
NE2 B:HIS39 4.4 39.9 1.0
CB B:ALA110 4.4 32.3 1.0
C B:ALA18 4.5 39.8 1.0
CB B:ALA18 4.6 36.0 1.0
CA B:CYS16 4.7 43.4 1.0
CA B:HIS39 4.7 42.6 1.0
CA B:ALA18 4.9 38.5 1.0
N B:ALA18 5.0 40.0 1.0

Zinc binding site 2 out of 6 in 5rm4

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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 Z1639162606


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 Z1639162606 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:60.9
occ:1.00
 SG B:CYS5 1.8 72.1 1.0
SG B:CYS26 2.1 64.1 1.0
SG B:CYS29 2.8 52.6 1.0
CB B:CYS8 2.9 68.2 1.0
SG B:CYS8 2.9 69.3 1.0
CB B:CYS5 3.0 71.5 1.0
CB B:CYS26 3.0 53.1 1.0
CB B:CYS29 3.2 45.9 1.0
N B:CYS8 3.6 66.3 1.0
N B:CYS26 3.7 60.9 1.0
CA B:CYS8 3.8 68.3 1.0
CA B:CYS26 3.9 58.2 1.0
CB B:SER10 4.1 50.7 1.0
N B:CYS29 4.2 48.0 1.0
CA B:CYS29 4.3 45.4 1.0
OG B:SER10 4.3 54.4 1.0
CA B:CYS5 4.4 69.4 1.0
O B:CYS26 4.4 67.9 1.0
C B:CYS26 4.6 60.0 1.0
CB B:LEU7 4.6 75.9 1.0
C B:LEU7 4.6 66.5 1.0
N B:GLY99 4.7 60.7 1.0
N B:ASN9 4.7 60.7 1.0
C B:CYS8 4.8 62.7 1.0
CA B:GLY99 4.9 55.8 1.0
C B:LEU25 4.9 55.1 1.0
C B:CYS5 4.9 69.5 1.0
CA B:LEU7 5.0 71.4 1.0
N B:LEU7 5.0 64.8 1.0

Zinc binding site 3 out of 6 in 5rm4

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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 Z1639162606


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 Z1639162606 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.0
occ:1.00
 SG B:CYS55 2.0 0.4 1.0
SG B:CYS50 2.6 84.8 1.0
CB B:CYS55 2.7 100.0 1.0
SG B:CYS72 2.8 85.6 1.0
ND1 B:HIS75 3.0 87.9 1.0
CB B:CYS50 3.3 93.1 1.0
CB B:CYS72 3.6 76.7 1.0
CE1 B:HIS75 3.8 90.1 1.0
CG B:HIS75 3.8 88.0 1.0
N B:CYS72 4.0 64.6 1.0
CB B:HIS75 4.0 89.5 1.0
CG2 B:VAL57 4.1 0.9 1.0
CB B:ALA52 4.2 0.2 1.0
CA B:CYS55 4.2 96.6 1.0
CA B:CYS72 4.4 73.5 1.0
CB B:VAL57 4.5 0.8 1.0
N B:HIS75 4.7 75.9 1.0
C B:CYS55 4.8 95.7 1.0
CA B:CYS50 4.8 92.1 1.0
NE2 B:HIS75 4.8 86.4 1.0
CD2 B:HIS75 4.8 80.3 1.0

Zinc binding site 4 out of 6 in 5rm4

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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 Z1639162606


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 Z1639162606 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:55.2
occ:1.00
 SG A:CYS55 2.1 46.9 1.0
SG A:CYS50 2.2 46.0 1.0
ND1 A:HIS75 2.3 44.5 1.0
SG A:CYS72 2.5 51.9 1.0
CB A:CYS55 3.0 49.2 1.0
CE1 A:HIS75 3.1 47.0 1.0
CB A:CYS50 3.1 51.4 1.0
CG A:HIS75 3.4 44.7 1.0
CB A:CYS72 3.4 48.9 1.0
CB A:HIS75 3.7 44.7 1.0
N A:CYS72 3.9 45.8 1.0
CB A:ALA52 4.1 49.3 1.0
CA A:CYS72 4.2 50.5 1.0
NE2 A:HIS75 4.3 45.3 1.0
CA A:CYS55 4.4 50.3 1.0
CD2 A:HIS75 4.4 44.1 1.0
CA A:CYS50 4.6 54.8 1.0
N A:HIS75 4.7 50.6 1.0
CG2 A:VAL57 4.7 69.9 1.0
CB A:VAL57 4.7 67.2 1.0
CA A:HIS75 4.8 46.8 1.0
C A:CYS72 5.0 54.8 1.0
CB A:SER74 5.0 56.0 1.0

Zinc binding site 5 out of 6 in 5rm4

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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 Z1639162606


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 Z1639162606 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:57.3
occ:1.00
 NE2 A:HIS33 1.7 34.4 1.0
ND1 A:HIS39 2.0 68.3 1.0
SG A:CYS16 2.3 71.1 1.0
SG A:CYS19 2.3 60.0 1.0
CE1 A:HIS33 2.7 35.9 1.0
CD2 A:HIS33 2.8 36.4 1.0
CE1 A:HIS39 3.0 68.4 1.0
CG A:HIS39 3.0 68.8 1.0
N A:CYS19 3.2 49.4 1.0
CB A:HIS39 3.3 68.0 1.0
CB A:CYS16 3.5 74.9 1.0
CB A:CYS19 3.6 53.2 1.0
CA A:CYS19 3.8 54.8 1.0
ND1 A:HIS33 3.8 36.2 1.0
CG A:HIS33 3.9 37.2 1.0
C A:ALA18 4.0 60.7 1.0
CB A:ALA18 4.1 70.5 1.0
NE2 A:HIS39 4.1 66.1 1.0
CD2 A:HIS39 4.1 69.8 1.0
CA A:ALA18 4.5 66.1 1.0
CB A:ALA110 4.5 45.3 1.0
N A:ALA18 4.7 66.5 1.0
O A:ALA18 4.8 70.2 1.0
CA A:HIS39 4.8 60.7 1.0
CA A:CYS16 4.9 78.0 1.0

Zinc binding site 6 out of 6 in 5rm4

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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 Z1639162606


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 Z1639162606 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:89.0
occ:1.00
 SG A:CYS26 2.4 97.9 1.0
SG A:CYS5 2.4 97.5 1.0
SG A:CYS29 2.7 81.5 1.0
SG A:CYS8 3.1 0.5 1.0
CB A:CYS26 3.3 0.2 1.0
CB A:CYS5 3.3 99.6 1.0
CB A:CYS8 3.3 0.6 1.0
CB A:CYS29 3.4 91.9 1.0
N A:CYS8 3.5 0.1 1.0
CA A:CYS8 3.9 0.5 1.0
N A:CYS26 4.0 96.7 1.0
CB A:LEU7 4.1 0.3 1.0
C A:LEU7 4.1 0.0 1.0
CA A:CYS26 4.2 97.9 1.0
CA A:LEU7 4.5 0.4 1.0
N A:LEU7 4.6 99.3 1.0
CA A:CYS5 4.7 0.6 1.0
CA A:CYS29 4.7 87.3 1.0
O A:CYS5 4.7 97.8 1.0
N A:ASN9 4.7 0.1 1.0
C A:CYS8 4.7 0.8 1.0
N A:CYS29 4.8 91.0 1.0
O A:CYS26 4.8 93.9 1.0
C A:CYS5 4.8 0.1 1.0
C A:CYS26 4.9 96.1 1.0
O A:LEU7 4.9 0.1 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 04:17:41 2024

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