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Zinc in PDB 5rlm: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1650168321

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1650168321

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1650168321:
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 Z1650168321, PDB code: 5rlm 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) 81.39 / 1.86
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.176, 70.115, 85.502, 102.84, 96.42, 112.11
R / Rfree (%) 17.3 / 23.7

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 Z1650168321 (pdb code 5rlm). 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 Z1650168321, PDB code: 5rlm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlm

Go back to Zinc Binding Sites List in 5rlm
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1650168321


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 Z1650168321 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:74.8
occ:1.00
 ND1 A:HIS75 2.3 67.7 1.0
SG A:CYS55 2.3 80.7 1.0
SG A:CYS50 2.3 70.2 1.0
SG A:CYS72 2.9 67.9 1.0
CB A:CYS50 3.2 70.9 1.0
CE1 A:HIS75 3.2 69.1 1.0
CG A:HIS75 3.3 65.8 1.0
CB A:CYS55 3.3 82.9 1.0
CB A:CYS72 3.5 71.1 1.0
CB A:HIS75 3.6 61.3 1.0
N A:CYS72 3.8 66.9 1.0
CB A:ALA52 4.2 61.5 1.0
CA A:CYS72 4.2 68.6 1.0
NE2 A:HIS75 4.4 67.1 1.0
CD2 A:HIS75 4.4 65.6 1.0
N A:HIS75 4.5 65.2 1.0
CG2 A:VAL57 4.6 71.3 1.0
CA A:CYS50 4.7 71.0 1.0
CA A:HIS75 4.7 63.3 1.0
CA A:CYS55 4.7 84.2 1.0
CB A:VAL57 4.7 71.8 1.0
C A:TYR71 4.9 62.4 1.0
C A:CYS72 5.0 72.8 1.0

Zinc binding site 2 out of 6 in 5rlm

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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 Z1650168321


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 Z1650168321 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:71.0
occ:1.00
 NE2 A:HIS33 1.9 63.6 1.0
ND1 A:HIS39 2.1 79.1 1.0
SG A:CYS19 2.3 74.2 1.0
SG A:CYS16 2.5 86.3 1.0
CE1 A:HIS33 2.9 65.5 1.0
CD2 A:HIS33 3.0 68.1 1.0
CG A:HIS39 3.0 78.7 1.0
CE1 A:HIS39 3.1 79.1 1.0
CB A:HIS39 3.4 74.5 1.0
CB A:CYS19 3.5 69.6 1.0
N A:CYS19 3.5 68.8 1.0
CB A:CYS16 3.6 88.9 1.0
CA A:CYS19 3.9 71.7 1.0
ND1 A:HIS33 4.0 68.8 1.0
CG A:HIS33 4.1 69.8 1.0
CD2 A:HIS39 4.2 80.5 1.0
NE2 A:HIS39 4.2 81.7 1.0
C A:ALA18 4.2 71.6 1.0
CB A:ALA110 4.4 67.9 1.0
CB A:ALA18 4.4 71.3 1.0
CA A:ALA18 4.7 73.3 1.0
N A:ALA18 4.8 73.0 1.0
CE2 A:PHE106 4.8 70.2 1.0
CA A:HIS39 4.9 73.1 1.0
CZ A:PHE106 4.9 70.2 1.0
O A:ALA18 4.9 74.1 1.0
CA A:CYS16 4.9 88.2 1.0

Zinc binding site 3 out of 6 in 5rlm

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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 Z1650168321


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 Z1650168321 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.0
occ:1.00
 SG A:CYS5 2.2 93.9 1.0
SG A:CYS29 2.4 98.0 1.0
SG A:CYS26 2.5 97.6 1.0
SG A:CYS8 2.6 0.1 1.0
CB A:CYS29 3.1 92.1 1.0
N A:CYS8 3.5 0.6 1.0
CB A:CYS5 3.5 94.2 1.0
CB A:CYS26 3.5 96.5 1.0
CB A:CYS8 3.6 0.6 1.0
N A:CYS26 3.9 91.0 1.0
CA A:CYS8 4.0 0.1 1.0
CB A:LEU7 4.1 0.3 1.0
CA A:CYS26 4.2 98.3 1.0
C A:LEU7 4.3 0.5 1.0
CA A:CYS29 4.4 88.5 1.0
N A:CYS29 4.4 91.0 1.0
CA A:LEU7 4.5 0.7 1.0
N A:LEU7 4.6 0.1 1.0
C A:CYS8 4.6 0.7 1.0
CB A:SER10 4.8 0.5 1.0
CA A:CYS5 4.8 94.9 1.0
N A:ASN9 4.9 0.1 1.0
C A:CYS26 4.9 0.4 1.0
OG A:SER10 5.0 0.9 1.0

Zinc binding site 4 out of 6 in 5rlm

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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 Z1650168321


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 Z1650168321 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:56.6
occ:1.00
 NE2 B:HIS33 2.0 52.9 1.0
ND1 B:HIS39 2.1 61.6 1.0
SG B:CYS16 2.2 60.8 1.0
SG B:CYS19 2.5 57.4 1.0
CD2 B:HIS33 3.0 52.7 1.0
CE1 B:HIS33 3.0 52.2 1.0
CG B:HIS39 3.0 61.8 1.0
CE1 B:HIS39 3.1 61.6 1.0
CB B:CYS16 3.3 61.3 1.0
CB B:HIS39 3.3 60.2 1.0
CB B:CYS19 3.4 54.4 1.0
N B:CYS19 3.4 56.1 1.0
CA B:CYS19 3.7 55.4 1.0
CG B:HIS33 4.1 53.7 1.0
C B:ALA18 4.1 56.3 1.0
ND1 B:HIS33 4.1 52.0 1.0
CD2 B:HIS39 4.2 61.2 1.0
NE2 B:HIS39 4.2 61.3 1.0
CB B:ALA18 4.4 53.5 1.0
CB B:ALA110 4.5 46.9 1.0
CA B:CYS16 4.6 62.2 1.0
CA B:ALA18 4.6 55.1 1.0
N B:ALA18 4.7 57.2 1.0
CA B:HIS39 4.8 58.4 1.0
O B:ALA18 4.9 54.5 1.0
C B:CYS16 5.0 61.8 1.0

Zinc binding site 5 out of 6 in 5rlm

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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 Z1650168321


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 Z1650168321 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:75.7
occ:1.00
 SG B:CYS5 2.3 71.3 1.0
SG B:CYS26 2.3 78.4 1.0
SG B:CYS29 2.5 74.6 1.0
CB B:CYS8 2.6 87.4 1.0
CB B:CYS29 3.1 63.7 1.0
SG B:CYS8 3.2 94.6 1.0
CB B:CYS26 3.4 76.3 1.0
CB B:CYS5 3.4 75.2 1.0
N B:CYS8 3.8 83.6 1.0
N B:CYS26 3.8 74.0 1.0
CA B:CYS8 3.8 85.8 1.0
N B:CYS29 4.1 63.3 1.0
CA B:CYS26 4.1 74.8 1.0
CA B:CYS29 4.2 62.0 1.0
N B:GLY99 4.5 80.0 1.0
CA B:GLY99 4.5 81.4 1.0
CB B:LEU7 4.6 77.4 1.0
C B:LEU7 4.7 79.7 1.0
CB B:SER10 4.7 78.2 1.0
C B:CYS26 4.8 75.8 1.0
OG B:SER10 4.8 74.4 1.0
CA B:CYS5 4.8 75.5 1.0
C B:CYS8 4.9 84.3 1.0
O B:CYS26 4.9 72.7 1.0
C B:GLY99 4.9 79.8 1.0
C B:LEU25 4.9 72.1 1.0
OG B:SER100 5.0 84.2 1.0

Zinc binding site 6 out of 6 in 5rlm

Go back to Zinc Binding Sites List in 5rlm
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1650168321


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 Z1650168321 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:98.4
occ:1.00
 SG B:CYS50 2.3 96.6 1.0
SG B:CYS55 2.4 0.7 1.0
ND1 B:HIS75 2.8 98.5 1.0
SG B:CYS72 2.9 95.6 1.0
CB B:CYS50 3.3 0.7 1.0
CB B:CYS55 3.3 0.7 1.0
CB B:HIS75 3.4 94.8 1.0
CG B:HIS75 3.5 98.3 1.0
CB B:CYS72 3.5 90.1 1.0
N B:CYS72 3.8 88.8 1.0
CE1 B:HIS75 3.9 0.3 1.0
CB B:ALA52 4.1 0.3 1.0
CA B:CYS72 4.2 89.9 1.0
N B:HIS75 4.4 92.6 1.0
CA B:HIS75 4.5 94.3 1.0
CA B:CYS50 4.7 0.9 1.0
CG2 B:VAL57 4.7 0.1 1.0
CD2 B:HIS75 4.7 99.7 1.0
CA B:CYS55 4.8 0.7 1.0
CB B:VAL57 4.8 0.1 1.0
C B:TYR71 4.9 87.2 1.0
NE2 B:HIS75 4.9 0.2 1.0
C B:CYS72 4.9 92.4 1.0
C B:SER74 5.0 94.2 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 04:00:42 2024

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