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Zinc in PDB 5rma: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z321318226

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z321318226

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z321318226:
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 Z321318226, PDB code: 5rma 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) 62.29 / 1.89
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.144, 70.211, 85.599, 102.82, 96.42, 112.16
R / Rfree (%) 17.6 / 23.6

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 Z321318226 (pdb code 5rma). 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 Z321318226, PDB code: 5rma:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rma

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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 Z321318226


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 Z321318226 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:66.8
occ:1.00
 SG A:CYS50 2.3 65.8 1.0
SG A:CYS55 2.4 68.2 1.0
ND1 A:HIS75 2.5 59.3 1.0
SG A:CYS72 2.7 64.7 1.0
CB A:CYS50 3.1 71.3 1.0
CB A:CYS55 3.3 73.9 1.0
CG A:HIS75 3.4 59.2 1.0
CB A:CYS72 3.4 69.6 1.0
CE1 A:HIS75 3.5 59.2 1.0
CB A:HIS75 3.5 58.1 1.0
N A:CYS72 3.7 66.1 1.0
CA A:CYS72 4.1 67.3 1.0
CB A:ALA52 4.3 65.5 1.0
N A:HIS75 4.4 61.3 1.0
CG2 A:VAL57 4.5 68.7 1.0
CD2 A:HIS75 4.5 56.1 1.0
NE2 A:HIS75 4.5 57.1 1.0
CA A:CYS50 4.6 70.0 1.0
CA A:HIS75 4.6 59.9 1.0
CB A:VAL57 4.6 72.2 1.0
CA A:CYS55 4.7 75.1 1.0
C A:TYR71 4.8 63.8 1.0
C A:CYS72 4.9 68.6 1.0

Zinc binding site 2 out of 6 in 5rma

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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 Z321318226


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 Z321318226 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:69.7
occ:1.00
 NE2 A:HIS33 1.9 62.5 1.0
ND1 A:HIS39 2.1 80.5 1.0
SG A:CYS16 2.3 93.5 1.0
SG A:CYS19 2.5 75.9 1.0
CD2 A:HIS33 2.9 65.3 1.0
CE1 A:HIS33 3.0 64.8 1.0
CG A:HIS39 3.1 82.3 1.0
CE1 A:HIS39 3.1 80.2 1.0
CB A:CYS16 3.3 88.0 1.0
CB A:HIS39 3.3 77.3 1.0
CB A:CYS19 3.6 72.5 1.0
N A:CYS19 3.6 74.2 1.0
CA A:CYS19 3.9 75.4 1.0
CG A:HIS33 4.1 67.2 1.0
ND1 A:HIS33 4.1 65.8 1.0
CD2 A:HIS39 4.3 82.1 1.0
C A:ALA18 4.3 78.7 1.0
NE2 A:HIS39 4.3 82.6 1.0
CB A:ALA110 4.4 64.3 1.0
CB A:ALA18 4.5 78.3 1.0
CA A:CYS16 4.7 88.6 1.0
CA A:ALA18 4.8 79.4 1.0
CE2 A:PHE106 4.8 71.6 1.0
CA A:HIS39 4.8 75.3 1.0
N A:ALA18 4.8 79.4 1.0
CZ A:PHE106 4.9 72.0 1.0
O A:ALA18 5.0 80.6 1.0

Zinc binding site 3 out of 6 in 5rma

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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 Z321318226


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 Z321318226 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.1
occ:1.00
 SG A:CYS5 2.2 0.9 1.0
SG A:CYS29 2.5 0.9 1.0
SG A:CYS8 2.5 0.9 1.0
SG A:CYS26 2.5 95.4 1.0
CB A:CYS5 3.3 0.7 1.0
CB A:CYS29 3.3 0.8 1.0
CB A:CYS8 3.3 0.8 1.0
N A:CYS8 3.4 0.3 1.0
CB A:CYS26 3.6 0.5 1.0
CA A:CYS8 3.8 0.3 1.0
N A:CYS26 4.0 97.8 1.0
CB A:LEU7 4.2 0.5 1.0
C A:LEU7 4.3 0.3 1.0
N A:CYS29 4.4 0.9 1.0
CA A:CYS26 4.4 0.1 1.0
C A:CYS8 4.4 0.2 1.0
CA A:CYS29 4.5 96.1 1.0
CA A:LEU7 4.6 0.5 1.0
N A:LEU7 4.6 0.0 1.0
N A:ASN9 4.7 0.1 1.0
CA A:CYS5 4.7 0.2 1.0
OG A:SER10 4.8 0.3 1.0
CB A:SER10 4.8 0.1 1.0
N A:SER10 5.0 0.1 1.0

Zinc binding site 4 out of 6 in 5rma

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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 Z321318226


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 Z321318226 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:49.7
occ:1.00
 NE2 B:HIS33 2.0 47.9 1.0
ND1 B:HIS39 2.1 50.0 1.0
SG B:CYS16 2.2 53.5 1.0
SG B:CYS19 2.5 52.1 1.0
CD2 B:HIS33 3.0 46.7 1.0
CG B:HIS39 3.0 51.7 1.0
CE1 B:HIS33 3.1 46.8 1.0
CE1 B:HIS39 3.1 52.0 1.0
CB B:HIS39 3.3 49.6 1.0
CB B:CYS16 3.3 51.1 1.0
N B:CYS19 3.5 50.0 1.0
CB B:CYS19 3.5 51.8 1.0
CA B:CYS19 3.8 52.1 1.0
C B:ALA18 4.1 49.6 1.0
CG B:HIS33 4.2 47.8 1.0
ND1 B:HIS33 4.2 46.4 1.0
CD2 B:HIS39 4.2 52.8 1.0
NE2 B:HIS39 4.2 52.7 1.0
CB B:ALA18 4.5 46.6 1.0
CB B:ALA110 4.5 45.6 1.0
CA B:ALA18 4.7 49.5 1.0
CA B:CYS16 4.7 52.0 1.0
N B:ALA18 4.8 50.9 1.0
CA B:HIS39 4.8 50.4 1.0
O B:ALA18 4.9 48.7 1.0
CE2 B:PHE106 4.9 49.0 1.0
C B:CYS16 5.0 52.9 1.0

Zinc binding site 5 out of 6 in 5rma

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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 Z321318226


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 Z321318226 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:63.8
occ:1.00
 SG B:CYS5 2.4 61.4 1.0
SG B:CYS29 2.4 58.5 1.0
SG B:CYS26 2.5 60.0 1.0
CB B:CYS8 2.7 83.0 1.0
SG B:CYS8 3.0 91.9 1.0
CB B:CYS29 3.0 55.7 1.0
CB B:CYS5 3.5 68.2 1.0
CB B:CYS26 3.7 60.0 1.0
N B:CYS8 3.8 79.6 1.0
CA B:CYS8 3.9 82.5 1.0
N B:CYS26 4.0 58.4 1.0
N B:CYS29 4.0 55.5 1.0
CA B:CYS29 4.1 54.2 1.0
CA B:CYS26 4.4 57.3 1.0
CB B:LEU7 4.5 71.8 1.0
C B:LEU7 4.6 75.2 1.0
N B:GLY99 4.6 78.4 1.0
CA B:GLY99 4.7 80.0 1.0
OG B:SER10 4.7 70.3 1.0
CB B:SER10 4.8 72.0 1.0
C B:CYS8 4.9 82.9 1.0
CA B:LEU7 4.9 72.8 1.0
CA B:CYS5 5.0 68.1 1.0
N B:LEU7 5.0 70.3 1.0
C B:CYS26 5.0 59.3 1.0

Zinc binding site 6 out of 6 in 5rma

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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 Z321318226


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 Z321318226 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:82.2
occ:1.00
 SG B:CYS50 2.2 80.0 1.0
SG B:CYS55 2.3 0.1 1.0
ND1 B:HIS75 2.5 89.1 1.0
SG B:CYS72 2.9 81.2 1.0
CB B:CYS50 3.1 84.0 1.0
CB B:CYS55 3.1 0.5 1.0
CG B:HIS75 3.4 87.6 1.0
CE1 B:HIS75 3.4 89.5 1.0
CB B:CYS72 3.5 74.8 1.0
CB B:HIS75 3.6 83.5 1.0
N B:CYS72 3.8 75.3 1.0
CB B:ALA52 4.2 0.1 1.0
CA B:CYS72 4.2 75.6 1.0
CD2 B:HIS75 4.5 90.5 1.0
CG2 B:VAL57 4.5 88.1 1.0
N B:HIS75 4.5 81.7 1.0
CA B:CYS50 4.5 83.6 1.0
NE2 B:HIS75 4.5 91.8 1.0
CA B:CYS55 4.6 0.2 1.0
CB B:VAL57 4.6 89.1 1.0
CA B:HIS75 4.7 83.3 1.0
C B:TYR71 4.9 74.1 1.0
C B:CYS72 5.0 78.1 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: Thu Aug 21 07:24:09 2025

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