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Zinc in PDB 5rlt: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53116498

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53116498

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z53116498:
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 Z53116498, PDB code: 5rlt 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 / 2.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.012, 70.286, 85.452, 102.69, 96.40, 112.44
R / Rfree (%) 15.1 / 26.4

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 Z53116498 (pdb code 5rlt). 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 Z53116498, PDB code: 5rlt:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlt

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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 Z53116498


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 Z53116498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:85.3
occ:1.00
 ND1 A:HIS75 2.3 73.7 1.0
SG A:CYS50 2.3 87.8 1.0
SG A:CYS55 2.4 91.0 1.0
SG A:CYS72 2.6 90.5 1.0
CE1 A:HIS75 3.2 73.4 1.0
CB A:CYS50 3.2 92.5 1.0
CB A:CYS55 3.3 92.7 1.0
CG A:HIS75 3.3 73.0 1.0
CB A:CYS72 3.4 89.0 1.0
CB A:HIS75 3.6 74.5 1.0
N A:CYS72 3.8 81.1 1.0
CA A:CYS72 4.1 86.1 1.0
CB A:ALA52 4.3 87.5 1.0
NE2 A:HIS75 4.4 72.2 1.0
N A:HIS75 4.4 79.2 1.0
CG2 A:VAL57 4.4 76.3 1.0
CD2 A:HIS75 4.4 71.0 1.0
CB A:VAL57 4.6 77.0 1.0
CA A:HIS75 4.7 78.0 1.0
CA A:CYS50 4.7 93.9 1.0
CA A:CYS55 4.7 94.5 1.0
C A:CYS72 4.9 91.3 1.0
C A:TYR71 4.9 76.1 1.0

Zinc binding site 2 out of 6 in 5rlt

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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 Z53116498


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 Z53116498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:81.2
occ:1.00
 NE2 A:HIS33 2.1 68.6 1.0
SG A:CYS16 2.4 98.8 1.0
ND1 A:HIS39 2.5 0.6 1.0
SG A:CYS19 2.5 84.9 1.0
CE1 A:HIS33 3.0 68.5 1.0
CD2 A:HIS33 3.1 69.2 1.0
CG A:HIS39 3.2 0.9 1.0
CE1 A:HIS39 3.3 0.9 1.0
CB A:CYS19 3.3 86.1 1.0
CB A:CYS16 3.4 95.0 1.0
CB A:HIS39 3.5 98.7 1.0
N A:CYS19 3.6 95.0 1.0
CA A:CYS19 3.8 92.4 1.0
CD2 A:HIS39 4.1 0.7 1.0
ND1 A:HIS33 4.1 68.7 1.0
NE2 A:HIS39 4.2 0.4 1.0
CG A:HIS33 4.2 71.5 1.0
CB A:ALA110 4.3 76.6 1.0
C A:ALA18 4.3 99.6 1.0
CB A:ALA18 4.7 99.2 1.0
CA A:CYS16 4.8 94.5 1.0
CA A:ALA18 4.9 98.3 1.0
CE2 A:PHE106 4.9 0.1 1.0
CA A:HIS39 4.9 92.1 1.0
O A:ALA18 4.9 98.3 1.0
N A:ALA18 5.0 94.8 1.0

Zinc binding site 3 out of 6 in 5rlt

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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 Z53116498


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 Z53116498 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.8
occ:1.00
 SG A:CYS5 2.2 0.1 1.0
SG A:CYS26 2.4 0.8 1.0
SG A:CYS8 2.6 0.7 1.0
SG A:CYS29 3.1 0.4 1.0
CB A:CYS5 3.2 0.1 1.0
CB A:CYS26 3.3 0.4 1.0
N A:CYS8 3.3 0.7 1.0
CB A:CYS8 3.5 0.9 1.0
CB A:CYS29 3.5 0.6 1.0
CA A:CYS8 3.8 0.1 1.0
N A:CYS26 3.9 0.7 1.0
CA A:CYS26 4.2 0.2 1.0
CB A:LEU7 4.2 0.4 1.0
C A:LEU7 4.3 0.7 1.0
C A:CYS8 4.3 0.2 1.0
N A:ASN9 4.3 0.7 1.0
CB A:SER10 4.6 0.1 1.0
CA A:CYS5 4.6 0.6 1.0
CA A:LEU7 4.6 0.7 1.0
N A:CYS29 4.6 0.9 1.0
OG A:SER10 4.6 0.9 1.0
N A:SER10 4.6 0.2 1.0
N A:LEU7 4.6 1.0 1.0
CA A:CYS29 4.7 0.8 1.0

Zinc binding site 4 out of 6 in 5rlt

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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 Z53116498


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 Z53116498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:48.6
occ:1.00
 NE2 B:HIS33 2.0 63.3 1.0
SG B:CYS16 2.3 61.4 1.0
ND1 B:HIS39 2.4 63.0 1.0
SG B:CYS19 2.7 55.6 1.0
CE1 B:HIS33 3.0 63.0 1.0
CD2 B:HIS33 3.0 63.4 1.0
CG B:HIS39 3.1 63.7 1.0
CE1 B:HIS39 3.3 62.6 1.0
CB B:HIS39 3.3 61.3 1.0
CB B:CYS16 3.4 62.4 1.0
CB B:CYS19 3.5 64.6 1.0
N B:CYS19 3.6 68.1 1.0
CA B:CYS19 3.9 66.0 1.0
CD2 B:HIS39 4.0 65.4 1.0
ND1 B:HIS33 4.1 61.5 1.0
CG B:HIS33 4.1 62.5 1.0
NE2 B:HIS39 4.2 65.9 1.0
C B:ALA18 4.3 67.5 1.0
CB B:ALA110 4.4 61.1 1.0
CB B:ALA18 4.6 60.4 1.0
CA B:HIS39 4.8 61.6 1.0
CA B:CYS16 4.8 63.4 1.0
CA B:ALA18 4.8 64.4 1.0
N B:ALA18 4.9 63.1 1.0
CE2 B:PHE106 5.0 64.0 1.0
O B:ALA18 5.0 71.8 1.0

Zinc binding site 5 out of 6 in 5rlt

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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 Z53116498


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 Z53116498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:87.6
occ:1.00
 SG B:CYS26 2.3 76.9 1.0
SG B:CYS5 2.4 77.5 1.0
CB B:CYS8 2.6 0.4 1.0
SG B:CYS29 2.7 69.1 1.0
CB B:CYS29 3.2 68.2 1.0
CB B:CYS26 3.3 76.5 1.0
SG B:CYS8 3.3 0.1 1.0
CB B:CYS5 3.4 84.8 1.0
N B:CYS8 3.5 0.8 1.0
CA B:CYS8 3.6 97.9 1.0
N B:CYS26 3.8 77.7 1.0
CA B:CYS26 4.1 76.5 1.0
N B:CYS29 4.3 71.4 1.0
CA B:CYS29 4.3 68.8 1.0
C B:LEU7 4.4 99.6 1.0
CB B:LEU7 4.4 96.2 1.0
C B:CYS8 4.5 98.3 1.0
OG B:SER10 4.5 86.2 1.0
CB B:SER10 4.6 89.0 1.0
N B:ASN9 4.7 94.7 1.0
CA B:LEU7 4.8 96.3 1.0
CA B:CYS5 4.8 85.2 1.0
N B:LEU7 4.8 96.8 1.0
N B:SER10 4.8 90.7 1.0
C B:CYS26 4.9 79.7 1.0
O B:CYS26 4.9 81.2 1.0
N B:GLY99 4.9 97.3 1.0

Zinc binding site 6 out of 6 in 5rlt

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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 Z53116498


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 Z53116498 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:89.0
occ:1.00
 SG B:CYS50 2.1 82.5 1.0
ND1 B:HIS75 2.2 82.2 1.0
SG B:CYS55 2.4 96.7 1.0
SG B:CYS72 2.7 73.3 1.0
CB B:CYS50 3.2 85.8 1.0
CE1 B:HIS75 3.2 82.2 1.0
CG B:HIS75 3.2 81.1 1.0
CB B:CYS55 3.2 94.8 1.0
CB B:CYS72 3.5 73.2 1.0
CB B:HIS75 3.5 78.5 1.0
N B:CYS72 3.8 74.8 1.0
CB B:ALA52 4.1 0.7 1.0
CA B:CYS72 4.2 76.8 1.0
NE2 B:HIS75 4.3 82.1 1.0
CD2 B:HIS75 4.4 81.1 1.0
N B:HIS75 4.4 77.8 1.0
CG2 B:VAL57 4.5 75.3 1.0
CA B:CYS50 4.6 87.7 1.0
CA B:HIS75 4.6 78.8 1.0
CA B:CYS55 4.7 97.6 1.0
CB B:VAL57 4.7 76.2 1.0
C B:TYR71 4.9 72.5 1.0
C B:CYS72 4.9 78.5 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: Wed Dec 16 07:30:22 2020

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