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Zinc in PDB 5rls: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z59181945

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z59181945

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z59181945:
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 Z59181945, PDB code: 5rls 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 / 2.28
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.176, 70.314, 85.289, 102.47, 96.41, 112.58
R / Rfree (%) 15.6 / 25.4

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 Z59181945 (pdb code 5rls). 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 Z59181945, PDB code: 5rls:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rls

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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 Z59181945


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 Z59181945 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.2
occ:1.00
 SG A:CYS50 2.3 73.6 1.0
ND1 A:HIS75 2.3 72.4 1.0
SG A:CYS55 2.3 85.1 1.0
SG A:CYS72 2.6 79.6 1.0
CB A:CYS50 3.1 77.8 1.0
CB A:CYS72 3.2 76.8 1.0
CG A:HIS75 3.3 71.4 1.0
CB A:CYS55 3.3 89.0 1.0
CE1 A:HIS75 3.3 71.3 1.0
CB A:HIS75 3.6 71.0 1.0
N A:CYS72 3.6 72.5 1.0
CA A:CYS72 4.0 77.4 1.0
CB A:ALA52 4.3 77.1 1.0
CG2 A:VAL57 4.4 77.9 1.0
N A:HIS75 4.4 76.1 1.0
NE2 A:HIS75 4.5 69.8 1.0
CD2 A:HIS75 4.5 70.6 1.0
CB A:VAL57 4.5 77.4 1.0
CA A:CYS50 4.6 82.3 1.0
CA A:HIS75 4.6 73.6 1.0
CA A:CYS55 4.7 92.5 1.0
C A:TYR71 4.8 72.6 1.0
C A:CYS72 4.8 78.9 1.0

Zinc binding site 2 out of 6 in 5rls

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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 Z59181945


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 Z59181945 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:76.9
occ:1.00
 NE2 A:HIS33 1.9 68.4 1.0
ND1 A:HIS39 2.3 93.9 1.0
SG A:CYS19 2.4 76.3 1.0
SG A:CYS16 2.4 86.2 1.0
CE1 A:HIS33 2.6 67.8 1.0
CG A:HIS39 3.1 94.3 1.0
CD2 A:HIS33 3.1 69.9 1.0
CE1 A:HIS39 3.2 95.1 1.0
CB A:CYS16 3.4 92.1 1.0
CB A:HIS39 3.4 90.7 1.0
CB A:CYS19 3.6 76.2 1.0
N A:CYS19 3.7 80.7 1.0
ND1 A:HIS33 3.9 69.4 1.0
CA A:CYS19 4.0 80.3 1.0
CG A:HIS33 4.1 71.8 1.0
CD2 A:HIS39 4.2 95.0 1.0
NE2 A:HIS39 4.2 95.6 1.0
C A:ALA18 4.4 86.0 1.0
CB A:ALA110 4.4 66.7 1.0
CB A:ALA18 4.7 84.5 1.0
CA A:CYS16 4.8 91.3 1.0
CA A:HIS39 4.9 85.8 1.0
CE2 A:PHE106 4.9 91.3 1.0
CA A:ALA18 4.9 86.9 1.0

Zinc binding site 3 out of 6 in 5rls

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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 Z59181945


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 Z59181945 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.2
occ:1.00
 SG A:CYS5 2.2 0.7 1.0
SG A:CYS26 2.3 0.1 1.0
SG A:CYS8 2.4 0.1 1.0
SG A:CYS29 2.7 0.4 1.0
CB A:CYS5 3.2 0.2 1.0
CB A:CYS26 3.3 0.1 1.0
CB A:CYS29 3.4 0.4 1.0
N A:CYS8 3.5 0.5 1.0
CB A:CYS8 3.6 0.8 1.0
N A:CYS26 3.9 0.1 1.0
CA A:CYS8 4.0 0.7 1.0
CA A:CYS26 4.2 0.9 1.0
C A:LEU7 4.2 0.8 1.0
CB A:LEU7 4.2 0.4 1.0
N A:CYS29 4.5 0.9 1.0
CA A:LEU7 4.5 0.3 1.0
N A:LEU7 4.5 0.4 1.0
CA A:CYS29 4.6 0.9 1.0
CA A:CYS5 4.6 0.3 1.0
C A:CYS8 4.6 0.1 1.0
CB A:SER10 4.6 0.2 1.0
OG A:SER10 4.7 0.8 1.0
N A:ASN9 4.7 0.9 1.0
N A:SER10 4.9 0.5 1.0
O A:CYS26 4.9 0.5 1.0
C A:CYS26 4.9 0.2 1.0

Zinc binding site 4 out of 6 in 5rls

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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 Z59181945


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 Z59181945 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:60.4
occ:1.00
 NE2 B:HIS33 2.0 67.7 1.0
ND1 B:HIS39 2.2 70.4 1.0
SG B:CYS16 2.2 67.6 1.0
SG B:CYS19 2.5 65.8 1.0
CE1 B:HIS33 2.9 67.7 1.0
CG B:HIS39 3.0 72.0 1.0
CD2 B:HIS33 3.2 67.1 1.0
CE1 B:HIS39 3.2 69.0 1.0
CB B:HIS39 3.3 70.7 1.0
CB B:CYS16 3.3 69.2 1.0
N B:CYS19 3.6 67.0 1.0
CB B:CYS19 3.6 65.7 1.0
CA B:CYS19 3.9 67.0 1.0
ND1 B:HIS33 4.1 68.0 1.0
CD2 B:HIS39 4.1 72.1 1.0
C B:ALA18 4.2 67.4 1.0
CG B:HIS33 4.2 67.8 1.0
NE2 B:HIS39 4.2 71.6 1.0
CB B:ALA18 4.5 60.8 1.0
CB B:ALA110 4.6 55.8 1.0
CA B:CYS16 4.6 68.6 1.0
CA B:ALA18 4.7 65.5 1.0
CA B:HIS39 4.7 69.9 1.0
N B:ALA18 4.8 63.7 1.0
O B:ALA18 4.9 68.2 1.0
C B:CYS16 5.0 69.2 1.0

Zinc binding site 5 out of 6 in 5rls

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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 Z59181945


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 Z59181945 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:87.7
occ:1.00
 SG B:CYS26 2.3 82.8 1.0
SG B:CYS5 2.3 84.6 1.0
SG B:CYS29 2.4 73.2 1.0
CB B:CYS8 2.6 96.0 1.0
CB B:CYS29 3.1 70.6 1.0
SG B:CYS8 3.1 0.8 1.0
CB B:CYS26 3.4 79.2 1.0
CB B:CYS5 3.4 91.7 1.0
N B:CYS8 3.5 94.2 1.0
CA B:CYS8 3.7 95.1 1.0
N B:CYS26 4.0 78.4 1.0
N B:CYS29 4.2 73.6 1.0
CA B:CYS26 4.2 77.9 1.0
CA B:CYS29 4.3 72.7 1.0
C B:LEU7 4.3 92.1 1.0
CB B:LEU7 4.4 88.7 1.0
N B:GLY99 4.6 86.5 1.0
C B:CYS8 4.7 96.9 1.0
OG B:SER10 4.7 83.2 1.0
CA B:LEU7 4.7 89.9 1.0
CB B:SER10 4.7 90.1 1.0
CA B:GLY99 4.8 86.1 1.0
N B:LEU7 4.8 88.7 1.0
O B:CYS26 4.8 83.2 1.0
CA B:CYS5 4.9 90.4 1.0
C B:CYS26 4.9 81.4 1.0
N B:ASN9 5.0 99.3 1.0

Zinc binding site 6 out of 6 in 5rls

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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 Z59181945


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 Z59181945 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:95.3
occ:1.00
 SG B:CYS50 2.2 83.3 1.0
SG B:CYS55 2.2 0.4 1.0
ND1 B:HIS75 2.4 93.9 1.0
SG B:CYS72 2.8 85.0 1.0
CB B:CYS50 3.0 90.7 1.0
CB B:CYS55 3.2 0.6 1.0
CE1 B:HIS75 3.3 93.7 1.0
CB B:CYS72 3.3 85.1 1.0
CG B:HIS75 3.4 91.8 1.0
CB B:HIS75 3.6 90.1 1.0
N B:CYS72 3.8 87.3 1.0
CA B:CYS72 4.1 87.2 1.0
CB B:ALA52 4.3 0.3 1.0
CG2 B:VAL57 4.4 98.3 1.0
NE2 B:HIS75 4.5 92.0 1.0
CB B:VAL57 4.5 96.9 1.0
CD2 B:HIS75 4.5 91.1 1.0
CA B:CYS50 4.5 92.7 1.0
N B:HIS75 4.6 88.3 1.0
CA B:CYS55 4.6 0.0 1.0
CA B:HIS75 4.7 87.9 1.0
C B:TYR71 4.9 87.5 1.0
C B:CYS72 5.0 87.1 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 04:06:32 2024

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