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Zinc in PDB 5rlk: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1509882419

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1509882419

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1509882419:
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 Z1509882419, PDB code: 5rlk 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) 81.53 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.129, 70.188, 85.558, 102.74, 96.23, 112.41
R / Rfree (%) 17.3 / 24

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 Z1509882419 (pdb code 5rlk). 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 Z1509882419, PDB code: 5rlk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlk

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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 Z1509882419


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 Z1509882419 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:61.4
occ:1.00
 SG A:CYS50 2.3 61.4 1.0
SG A:CYS55 2.3 66.4 1.0
ND1 A:HIS75 2.4 58.0 1.0
SG A:CYS72 2.6 59.0 1.0
CB A:CYS50 3.2 64.8 1.0
CB A:CYS55 3.3 69.2 1.0
CG A:HIS75 3.3 57.9 1.0
CE1 A:HIS75 3.4 57.8 1.0
CB A:CYS72 3.4 63.7 1.0
CB A:HIS75 3.5 56.3 1.0
N A:CYS72 3.8 63.6 1.0
CA A:CYS72 4.2 64.3 1.0
CB A:ALA52 4.2 63.9 1.0
N A:HIS75 4.5 61.1 1.0
CD2 A:HIS75 4.5 56.9 1.0
NE2 A:HIS75 4.5 57.3 1.0
CG2 A:VAL57 4.5 68.1 1.0
CA A:HIS75 4.7 58.7 1.0
CB A:VAL57 4.7 68.8 1.0
CA A:CYS50 4.7 66.3 1.0
CA A:CYS55 4.7 72.0 1.0
C A:TYR71 4.9 59.2 1.0
C A:CYS72 5.0 68.3 1.0

Zinc binding site 2 out of 6 in 5rlk

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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 Z1509882419


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 Z1509882419 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:62.6
occ:1.00
 ND1 A:HIS39 2.0 74.1 1.0
NE2 A:HIS33 2.1 55.7 1.0
SG A:CYS19 2.3 62.2 1.0
SG A:CYS16 2.4 75.4 1.0
CE1 A:HIS39 3.0 75.0 1.0
CE1 A:HIS33 3.0 57.4 1.0
CG A:HIS39 3.0 74.3 1.0
CD2 A:HIS33 3.1 59.0 1.0
CB A:CYS19 3.4 63.7 1.0
CB A:HIS39 3.4 70.2 1.0
CB A:CYS16 3.4 73.9 1.0
N A:CYS19 3.4 66.3 1.0
CA A:CYS19 3.7 66.5 1.0
C A:ALA18 4.1 70.9 1.0
NE2 A:HIS39 4.1 78.8 1.0
CD2 A:HIS39 4.2 76.7 1.0
ND1 A:HIS33 4.2 60.6 1.0
CG A:HIS33 4.2 60.5 1.0
CB A:ALA110 4.5 57.3 1.0
CB A:ALA18 4.5 73.1 1.0
CA A:ALA18 4.7 72.1 1.0
N A:ALA18 4.8 73.5 1.0
CA A:CYS16 4.8 73.4 1.0
O A:ALA18 4.8 72.8 1.0
CA A:HIS39 4.9 67.8 1.0
CE2 A:PHE106 4.9 61.3 1.0

Zinc binding site 3 out of 6 in 5rlk

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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 Z1509882419


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 Z1509882419 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:94.0
occ:1.00
 SG A:CYS5 2.2 85.3 1.0
SG A:CYS26 2.3 89.8 1.0
SG A:CYS8 2.6 0.9 1.0
SG A:CYS29 2.7 1.0 1.0
CB A:CYS29 3.2 92.5 1.0
CB A:CYS26 3.3 88.5 1.0
CB A:CYS5 3.4 87.8 1.0
N A:CYS8 3.6 98.8 1.0
CB A:CYS8 3.6 98.2 1.0
N A:CYS26 3.8 85.5 1.0
CA A:CYS8 4.1 99.5 1.0
CA A:CYS26 4.1 90.5 1.0
CB A:LEU7 4.2 92.4 1.0
C A:LEU7 4.4 97.9 1.0
N A:CYS29 4.4 88.1 1.0
CA A:CYS29 4.4 84.3 1.0
CA A:LEU7 4.6 91.4 1.0
C A:CYS8 4.6 0.8 1.0
N A:LEU7 4.6 88.5 1.0
CA A:CYS5 4.8 86.5 1.0
C A:CYS26 4.9 91.5 1.0
CB A:SER10 4.9 0.9 1.0
O A:CYS26 4.9 93.7 1.0
OG A:SER10 4.9 94.5 1.0
N A:ASN9 4.9 0.2 1.0

Zinc binding site 4 out of 6 in 5rlk

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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 Z1509882419


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 Z1509882419 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:56.1
occ:1.00
 NE2 B:HIS33 2.0 56.1 1.0
ND1 B:HIS39 2.0 50.8 1.0
SG B:CYS16 2.2 61.2 1.0
SG B:CYS19 2.4 54.5 1.0
CD2 B:HIS33 3.0 56.6 1.0
CG B:HIS39 3.0 55.5 1.0
CE1 B:HIS33 3.0 55.0 1.0
CE1 B:HIS39 3.1 52.8 1.0
CB B:HIS39 3.3 56.9 1.0
CB B:CYS16 3.4 59.5 1.0
CB B:CYS19 3.5 53.7 1.0
N B:CYS19 3.5 55.0 1.0
CA B:CYS19 3.8 54.3 1.0
CG B:HIS33 4.1 57.9 1.0
ND1 B:HIS33 4.2 55.2 1.0
C B:ALA18 4.2 53.5 1.0
CD2 B:HIS39 4.2 54.8 1.0
NE2 B:HIS39 4.2 51.8 1.0
CB B:ALA18 4.5 50.0 1.0
CB B:ALA110 4.6 45.9 1.0
CA B:ALA18 4.7 53.4 1.0
CA B:CYS16 4.7 61.2 1.0
N B:ALA18 4.8 58.0 1.0
CA B:HIS39 4.8 55.8 1.0
O B:ALA18 4.9 55.4 1.0

Zinc binding site 5 out of 6 in 5rlk

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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 Z1509882419


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 Z1509882419 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.9
occ:1.00
 SG B:CYS26 2.2 76.6 1.0
SG B:CYS5 2.4 82.1 1.0
SG B:CYS29 2.5 82.0 1.0
CB B:CYS29 2.9 76.1 1.0
CB B:CYS8 3.0 99.9 1.0
CB B:CYS26 3.3 79.2 1.0
SG B:CYS8 3.3 99.8 1.0
CB B:CYS5 3.6 88.7 1.0
N B:CYS26 3.8 78.9 1.0
N B:CYS8 3.8 0.4 1.0
CA B:CYS8 4.0 98.1 1.0
N B:CYS29 4.1 79.4 1.0
CA B:CYS26 4.1 80.6 1.0
CA B:CYS29 4.1 73.3 1.0
CB B:LEU7 4.4 94.8 1.0
C B:LEU7 4.5 97.8 1.0
C B:CYS26 4.7 83.2 1.0
O B:CYS26 4.7 82.5 1.0
N B:GLY99 4.8 87.4 1.0
CA B:LEU7 4.8 94.6 1.0
N B:LEU7 4.9 89.8 1.0
C B:LEU25 5.0 76.5 1.0
OG B:SER10 5.0 85.8 1.0
CB B:SER10 5.0 89.3 1.0
CA B:GLY99 5.0 89.5 1.0

Zinc binding site 6 out of 6 in 5rlk

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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 Z1509882419


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 Z1509882419 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:95.1
occ:1.00
 SG B:CYS50 2.2 85.4 1.0
SG B:CYS55 2.3 0.7 1.0
ND1 B:HIS75 2.3 92.4 1.0
SG B:CYS72 2.8 79.0 1.0
CB B:CYS55 3.2 0.7 1.0
CB B:CYS50 3.2 90.3 1.0
CG B:HIS75 3.3 91.0 1.0
CE1 B:HIS75 3.4 93.1 1.0
CB B:HIS75 3.5 88.8 1.0
CB B:CYS72 3.5 76.7 1.0
N B:CYS72 3.8 77.2 1.0
CB B:ALA52 4.0 0.8 1.0
CA B:CYS72 4.3 77.2 1.0
CD2 B:HIS75 4.5 93.2 1.0
N B:HIS75 4.5 84.9 1.0
NE2 B:HIS75 4.5 94.2 1.0
CA B:CYS50 4.6 90.4 1.0
CA B:HIS75 4.6 88.2 1.0
CA B:CYS55 4.6 0.4 1.0
CG2 B:VAL57 4.6 89.7 1.0
CB B:VAL57 4.7 91.7 1.0
C B:TYR71 4.9 76.8 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 04:00:43 2024

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