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Zinc in PDB 5rmi: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53860899

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53860899

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53860899:
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 Z53860899, PDB code: 5rmi 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) 81.32 / 2.12
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.113, 70.211, 85.247, 102.75, 95.95, 112.48
R / Rfree (%) 16.4 / 25.1

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 Z53860899 (pdb code 5rmi). 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 Z53860899, PDB code: 5rmi:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmi

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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 Z53860899


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 Z53860899 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.7
occ:1.00
 ND1 A:HIS75 2.2 64.5 1.0
SG A:CYS50 2.3 68.7 1.0
SG A:CYS55 2.3 87.6 1.0
SG A:CYS72 3.0 80.9 1.0
CE1 A:HIS75 3.2 63.8 1.0
CB A:CYS50 3.3 72.8 1.0
CG A:HIS75 3.3 62.9 1.0
CB A:CYS55 3.3 88.7 1.0
CB A:CYS72 3.5 77.0 1.0
CB A:HIS75 3.6 62.6 1.0
N A:CYS72 3.8 72.6 1.0
CA A:CYS72 4.2 73.7 1.0
CB A:ALA52 4.2 75.4 1.0
NE2 A:HIS75 4.3 61.1 1.0
CD2 A:HIS75 4.4 61.9 1.0
N A:HIS75 4.4 63.1 1.0
CG2 A:VAL57 4.5 77.5 1.0
CB A:VAL57 4.7 78.8 1.0
CA A:HIS75 4.7 63.6 1.0
CA A:CYS50 4.7 74.4 1.0
CA A:CYS55 4.7 91.2 1.0
C A:CYS72 4.9 76.0 1.0
CB A:SER74 4.9 68.7 1.0
C A:TYR71 5.0 69.2 1.0

Zinc binding site 2 out of 6 in 5rmi

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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 Z53860899


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 Z53860899 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:72.6
occ:1.00
 NE2 A:HIS33 1.9 65.2 1.0
ND1 A:HIS39 2.2 86.5 1.0
SG A:CYS16 2.3 88.0 1.0
SG A:CYS19 2.6 73.8 1.0
CE1 A:HIS33 2.9 65.9 1.0
CD2 A:HIS33 3.0 67.2 1.0
CG A:HIS39 3.1 87.1 1.0
CE1 A:HIS39 3.2 85.9 1.0
CB A:HIS39 3.4 83.8 1.0
CB A:CYS16 3.4 86.5 1.0
CB A:CYS19 3.5 74.0 1.0
N A:CYS19 3.6 78.0 1.0
CA A:CYS19 3.9 77.4 1.0
ND1 A:HIS33 4.0 67.7 1.0
CG A:HIS33 4.1 70.0 1.0
CD2 A:HIS39 4.3 87.7 1.0
C A:ALA18 4.3 81.5 1.0
NE2 A:HIS39 4.3 86.3 1.0
CB A:ALA110 4.4 62.8 1.0
CB A:ALA18 4.6 81.8 1.0
CE2 A:PHE106 4.8 81.5 1.0
CA A:CYS16 4.8 85.2 1.0
CA A:ALA18 4.8 81.5 1.0
CA A:HIS39 4.9 80.5 1.0
N A:ALA18 4.9 81.7 1.0
O A:ALA18 4.9 82.2 1.0
CZ A:PHE106 4.9 81.6 1.0

Zinc binding site 3 out of 6 in 5rmi

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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 Z53860899


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 Z53860899 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.4
occ:1.00
 SG A:CYS5 2.2 0.6 1.0
SG A:CYS26 2.2 100.0 1.0
SG A:CYS8 2.6 0.8 1.0
SG A:CYS29 2.8 0.7 1.0
CB A:CYS5 3.2 0.8 1.0
CB A:CYS29 3.3 0.1 1.0
N A:CYS8 3.4 0.8 1.0
CB A:CYS26 3.4 0.4 1.0
CB A:CYS8 3.6 0.2 1.0
N A:CYS26 3.9 0.2 1.0
CA A:CYS8 3.9 0.0 1.0
CB A:LEU7 4.2 0.5 1.0
CA A:CYS26 4.2 0.9 1.0
C A:LEU7 4.3 0.1 1.0
C A:CYS8 4.5 0.1 1.0
CA A:CYS29 4.5 95.3 1.0
CA A:LEU7 4.6 0.1 1.0
N A:CYS29 4.6 0.8 1.0
CA A:CYS5 4.6 0.4 1.0
N A:LEU7 4.6 0.8 1.0
CB A:SER10 4.6 0.5 1.0
N A:ASN9 4.7 0.1 1.0
OG A:SER10 4.7 0.0 1.0
N A:SER10 4.9 0.5 1.0
C A:CYS26 4.9 0.5 1.0

Zinc binding site 4 out of 6 in 5rmi

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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 Z53860899


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 Z53860899 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:53.9
occ:1.00
 NE2 B:HIS33 2.0 55.2 1.0
SG B:CYS16 2.1 57.5 1.0
ND1 B:HIS39 2.2 56.6 1.0
SG B:CYS19 2.6 60.4 1.0
CE1 B:HIS33 3.0 56.1 1.0
CD2 B:HIS33 3.0 55.7 1.0
CG B:HIS39 3.1 57.5 1.0
CE1 B:HIS39 3.3 57.3 1.0
CB B:CYS16 3.3 59.2 1.0
CB B:HIS39 3.3 56.4 1.0
CB B:CYS19 3.4 62.2 1.0
N B:CYS19 3.5 62.1 1.0
CA B:CYS19 3.8 62.9 1.0
CG B:HIS33 4.2 56.2 1.0
ND1 B:HIS33 4.2 55.9 1.0
C B:ALA18 4.2 61.0 1.0
CD2 B:HIS39 4.3 57.1 1.0
NE2 B:HIS39 4.3 58.4 1.0
CB B:ALA18 4.5 53.6 1.0
CB B:ALA110 4.6 45.6 1.0
CA B:CYS16 4.6 60.9 1.0
CA B:ALA18 4.7 58.7 1.0
N B:ALA18 4.8 61.3 1.0
CA B:HIS39 4.8 57.4 1.0
O B:ALA18 4.9 61.4 1.0
C B:CYS16 5.0 59.7 1.0
CE2 B:PHE106 5.0 57.9 1.0

Zinc binding site 5 out of 6 in 5rmi

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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 Z53860899


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 Z53860899 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:77.2
occ:1.00
 SG B:CYS26 2.2 68.2 1.0
SG B:CYS5 2.4 68.8 1.0
CB B:CYS8 2.5 92.4 1.0
SG B:CYS29 2.5 68.0 1.0
CB B:CYS29 3.1 64.0 1.0
SG B:CYS8 3.1 0.4 1.0
CB B:CYS5 3.5 72.6 1.0
CB B:CYS26 3.5 70.8 1.0
N B:CYS8 3.6 89.4 1.0
CA B:CYS8 3.7 89.9 1.0
N B:CYS26 3.9 68.7 1.0
N B:CYS29 4.1 64.9 1.0
CA B:CYS29 4.2 63.6 1.0
CA B:CYS26 4.2 69.1 1.0
CB B:LEU7 4.5 84.7 1.0
C B:LEU7 4.5 86.1 1.0
OG B:SER10 4.6 79.2 1.0
CB B:SER10 4.7 82.5 1.0
C B:CYS8 4.7 89.1 1.0
N B:GLY99 4.8 89.8 1.0
CA B:GLY99 4.8 87.9 1.0
CA B:LEU7 4.9 83.9 1.0
CA B:CYS5 4.9 73.5 1.0
C B:CYS26 4.9 72.8 1.0
N B:ASN9 4.9 88.3 1.0
O B:CYS26 4.9 72.7 1.0
N B:LEU7 4.9 79.8 1.0

Zinc binding site 6 out of 6 in 5rmi

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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 Z53860899


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 Z53860899 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:91.9
occ:1.00
 SG B:CYS50 2.2 89.9 1.0
ND1 B:HIS75 2.2 89.9 1.0
SG B:CYS55 2.4 0.9 1.0
SG B:CYS72 2.9 88.1 1.0
CE1 B:HIS75 3.2 88.4 1.0
CB B:CYS50 3.2 91.5 1.0
CG B:HIS75 3.3 88.5 1.0
CB B:CYS55 3.4 0.4 1.0
CB B:CYS72 3.4 85.4 1.0
CB B:HIS75 3.5 88.4 1.0
N B:CYS72 3.7 83.3 1.0
CA B:CYS72 4.1 86.1 1.0
CB B:ALA52 4.2 0.4 1.0
N B:HIS75 4.4 88.4 1.0
NE2 B:HIS75 4.4 88.3 1.0
CD2 B:HIS75 4.4 89.0 1.0
CG2 B:VAL57 4.5 91.1 1.0
CA B:HIS75 4.6 90.9 1.0
CA B:CYS50 4.7 91.8 1.0
CB B:VAL57 4.7 90.3 1.0
CA B:CYS55 4.8 0.9 1.0
C B:CYS72 4.9 88.9 1.0
C B:TYR71 4.9 80.2 1.0
CB B:SER74 5.0 85.3 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 07:27:09 2025

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