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Zinc in PDB 5rld: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19735981

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19735981

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19735981:
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 Z19735981, PDB code: 5rld 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) 62.37 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.423, 70.317, 85.425, 102.56, 96.36, 112.39
R / Rfree (%) 16.6 / 27

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 Z19735981 (pdb code 5rld). 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 Z19735981, PDB code: 5rld:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rld

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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 Z19735981


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 Z19735981 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:91.7
occ:1.00
 SG A:CYS55 2.2 90.3 1.0
SG A:CYS50 2.3 77.4 1.0
ND1 A:HIS75 2.3 74.1 1.0
CB A:CYS55 3.1 91.4 1.0
SG A:CYS72 3.2 93.9 1.0
CE1 A:HIS75 3.2 71.5 1.0
CB A:CYS50 3.3 81.7 1.0
CG A:HIS75 3.4 72.1 1.0
CB A:CYS72 3.6 86.9 1.0
CB A:HIS75 3.7 71.6 1.0
N A:CYS72 3.9 80.7 1.0
CB A:ALA52 4.0 81.0 1.0
CA A:CYS72 4.3 83.9 1.0
NE2 A:HIS75 4.4 68.0 1.0
CD2 A:HIS75 4.5 70.9 1.0
N A:HIS75 4.5 77.0 1.0
CA A:CYS55 4.6 96.4 1.0
CG2 A:VAL57 4.6 82.7 1.0
CA A:CYS50 4.7 84.0 1.0
CB A:VAL57 4.8 84.9 1.0
CA A:HIS75 4.8 75.2 1.0

Zinc binding site 2 out of 6 in 5rld

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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 Z19735981


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 Z19735981 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:80.2
occ:1.00
 NE2 A:HIS33 2.0 74.4 1.0
ND1 A:HIS39 2.3 0.6 1.0
SG A:CYS16 2.3 0.3 1.0
SG A:CYS19 2.6 88.5 1.0
CE1 A:HIS33 2.8 74.1 1.0
CG A:HIS39 3.0 0.2 1.0
CE1 A:HIS39 3.2 0.0 1.0
CD2 A:HIS33 3.2 76.2 1.0
CB A:HIS39 3.3 99.7 1.0
CB A:CYS19 3.4 88.2 1.0
CB A:CYS16 3.4 0.8 1.0
N A:CYS19 3.5 90.3 1.0
CA A:CYS19 3.7 91.8 1.0
CD2 A:HIS39 4.0 0.1 1.0
ND1 A:HIS33 4.0 75.4 1.0
NE2 A:HIS39 4.1 0.3 1.0
C A:ALA18 4.2 94.3 1.0
CG A:HIS33 4.2 77.3 1.0
CB A:ALA110 4.4 72.5 1.0
CB A:ALA18 4.6 95.7 1.0
CA A:ALA18 4.7 94.8 1.0
CA A:CYS16 4.8 0.1 1.0
CA A:HIS39 4.8 95.7 1.0
N A:ALA18 4.8 94.0 1.0
O A:ALA18 4.8 85.7 1.0

Zinc binding site 3 out of 6 in 5rld

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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 Z19735981


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 Z19735981 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.4
occ:1.00
 SG A:CYS29 2.3 0.1 1.0
SG A:CYS26 2.4 0.2 1.0
SG A:CYS8 2.5 0.0 1.0
CB A:CYS8 2.9 0.1 1.0
CB A:CYS29 3.0 0.6 1.0
SG A:CYS5 3.0 0.8 1.0
CB A:CYS26 3.6 0.5 1.0
N A:CYS8 3.9 0.6 1.0
CA A:CYS8 4.0 0.4 1.0
N A:CYS29 4.1 0.1 1.0
CA A:CYS29 4.1 0.5 1.0
CB A:CYS5 4.2 0.1 1.0
CB A:LEU7 4.4 0.9 1.0
N A:CYS26 4.4 1.0 1.0
C A:LEU7 4.4 0.4 1.0
CA A:CYS26 4.5 0.3 1.0
CA A:LEU7 4.9 0.7 1.0
O A:CYS26 4.9 0.6 1.0
OG A:SER10 4.9 0.8 1.0
O A:LEU7 4.9 0.3 1.0
C A:CYS8 5.0 0.1 1.0
C A:CYS26 5.0 0.2 1.0

Zinc binding site 4 out of 6 in 5rld

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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 Z19735981


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 Z19735981 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:62.1
occ:1.00
 NE2 B:HIS33 2.0 58.2 1.0
SG B:CYS16 2.2 65.7 1.0
ND1 B:HIS39 2.4 71.3 1.0
SG B:CYS19 2.6 62.8 1.0
CE1 B:HIS33 2.9 58.3 1.0
CG B:HIS39 3.1 72.3 1.0
CD2 B:HIS33 3.1 60.3 1.0
CB B:HIS39 3.3 73.1 1.0
CB B:CYS16 3.3 69.0 1.0
CE1 B:HIS39 3.3 70.7 1.0
CB B:CYS19 3.3 64.4 1.0
N B:CYS19 3.4 68.4 1.0
CA B:CYS19 3.7 68.8 1.0
ND1 B:HIS33 4.1 59.1 1.0
CD2 B:HIS39 4.1 71.7 1.0
C B:ALA18 4.2 70.9 1.0
CG B:HIS33 4.2 61.2 1.0
NE2 B:HIS39 4.2 70.8 1.0
CB B:ALA110 4.6 56.7 1.0
CB B:ALA18 4.6 65.2 1.0
CA B:CYS16 4.7 69.9 1.0
CA B:ALA18 4.7 69.1 1.0
N B:ALA18 4.7 68.2 1.0
CA B:HIS39 4.8 71.5 1.0
O B:ALA18 4.9 77.1 1.0
C B:CYS16 5.0 70.3 1.0

Zinc binding site 5 out of 6 in 5rld

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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 Z19735981


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 Z19735981 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.9
occ:1.00
 SG B:CYS26 2.2 89.0 1.0
SG B:CYS5 2.5 71.5 1.0
SG B:CYS29 2.7 74.5 1.0
CB B:CYS8 2.7 92.3 1.0
CB B:CYS29 3.2 71.7 1.0
CB B:CYS5 3.5 80.6 1.0
CB B:CYS26 3.5 85.0 1.0
SG B:CYS8 3.8 0.0 1.0
N B:CYS8 3.9 87.2 1.0
CA B:CYS8 3.9 88.6 1.0
N B:CYS26 4.0 79.6 1.0
N B:CYS29 4.1 76.0 1.0
CA B:CYS29 4.2 71.5 1.0
CA B:CYS26 4.3 82.3 1.0
N B:GLY99 4.3 85.1 1.0
CA B:GLY99 4.4 84.2 1.0
OG B:SER10 4.5 82.3 1.0
C B:LEU7 4.6 87.1 1.0
CB B:SER10 4.7 80.2 1.0
C B:CYS8 4.7 86.7 1.0
CB B:LEU7 4.8 88.8 1.0
N B:ASN9 4.9 87.7 1.0
O B:CYS26 4.9 81.5 1.0
C B:GLY99 4.9 82.2 1.0
C B:CYS26 4.9 83.8 1.0
CA B:CYS5 5.0 80.2 1.0
N B:SER10 5.0 85.3 1.0

Zinc binding site 6 out of 6 in 5rld

Go back to Zinc Binding Sites List in 5rld
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19735981


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 Z19735981 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:0.2
occ:1.00
 SG B:CYS50 2.2 99.0 1.0
SG B:CYS55 2.4 0.7 1.0
ND1 B:HIS75 2.4 96.6 1.0
SG B:CYS72 3.1 0.9 1.0
CB B:CYS50 3.3 0.2 1.0
CB B:CYS55 3.3 0.5 1.0
CG B:HIS75 3.4 95.7 1.0
CE1 B:HIS75 3.4 97.2 1.0
CB B:CYS72 3.5 98.7 1.0
CB B:HIS75 3.6 94.7 1.0
N B:CYS72 3.7 98.1 1.0
CB B:ALA52 4.0 0.4 1.0
CA B:CYS72 4.1 97.3 1.0
N B:HIS75 4.4 95.3 1.0
NE2 B:HIS75 4.5 0.3 1.0
CD2 B:HIS75 4.5 98.1 1.0
CG2 B:VAL57 4.5 0.2 1.0
CA B:HIS75 4.6 95.6 1.0
CA B:CYS50 4.7 0.9 1.0
CB B:VAL57 4.8 0.7 1.0
CA B:CYS55 4.8 0.3 1.0
C B:TYR71 4.9 96.4 1.0
C B:CYS72 4.9 96.0 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 03:58:16 2024

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