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Zinc in PDB 5rlq: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z285782452

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z285782452

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z285782452:
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 Z285782452, PDB code: 5rlq 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) 81.72 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.338, 70.474, 85.777, 102.76, 96.29, 112.26
R / Rfree (%) 15.5 / 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 Z285782452 (pdb code 5rlq). 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 Z285782452, PDB code: 5rlq:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlq

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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 Z285782452


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 Z285782452 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:82.5
occ:1.00
 SG A:CYS50 2.3 81.5 1.0
SG A:CYS55 2.3 89.0 1.0
ND1 A:HIS75 2.5 77.3 1.0
SG A:CYS72 2.8 78.7 1.0
CB A:CYS50 3.2 90.0 1.0
CB A:CYS55 3.4 96.6 1.0
CG A:HIS75 3.4 76.0 1.0
CB A:CYS72 3.4 84.3 1.0
CE1 A:HIS75 3.5 76.3 1.0
CB A:HIS75 3.6 74.9 1.0
N A:CYS72 3.9 79.5 1.0
CB A:ALA52 4.1 81.3 1.0
CA A:CYS72 4.2 83.3 1.0
CG2 A:VAL57 4.4 90.0 1.0
N A:HIS75 4.5 77.3 1.0
CD2 A:HIS75 4.5 75.2 1.0
NE2 A:HIS75 4.6 73.9 1.0
CA A:CYS50 4.7 88.5 1.0
CB A:VAL57 4.7 91.4 1.0
CA A:HIS75 4.7 75.9 1.0
CA A:CYS55 4.8 98.5 1.0
C A:CYS72 5.0 87.1 1.0

Zinc binding site 2 out of 6 in 5rlq

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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 Z285782452


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 Z285782452 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:78.4
occ:1.00
 ND1 A:HIS39 2.0 93.7 1.0
NE2 A:HIS33 2.0 77.0 1.0
SG A:CYS16 2.4 0.2 1.0
SG A:CYS19 2.6 81.8 1.0
CE1 A:HIS33 2.9 78.1 1.0
CE1 A:HIS39 3.0 95.8 1.0
CG A:HIS39 3.1 94.3 1.0
CD2 A:HIS33 3.1 80.7 1.0
CB A:HIS39 3.4 92.1 1.0
CB A:CYS16 3.5 95.0 1.0
CB A:CYS19 3.5 77.5 1.0
N A:CYS19 3.6 77.3 1.0
CA A:CYS19 3.9 82.0 1.0
ND1 A:HIS33 4.1 78.8 1.0
NE2 A:HIS39 4.1 96.7 1.0
CG A:HIS33 4.2 81.8 1.0
CD2 A:HIS39 4.2 96.3 1.0
C A:ALA18 4.2 82.6 1.0
CB A:ALA110 4.4 81.1 1.0
CB A:ALA18 4.5 81.5 1.0
CA A:ALA18 4.8 83.8 1.0
CA A:HIS39 4.9 89.0 1.0
CA A:CYS16 4.9 95.3 1.0
O A:ALA18 4.9 81.9 1.0
N A:ALA18 4.9 84.5 1.0
CE2 A:PHE106 4.9 94.9 1.0

Zinc binding site 3 out of 6 in 5rlq

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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 Z285782452


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 Z285782452 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.7
occ:1.00
 SG A:CYS26 2.3 1.0 1.0
SG A:CYS5 2.4 0.3 1.0
SG A:CYS29 2.5 0.9 1.0
SG A:CYS8 2.5 0.9 1.0
CB A:CYS29 3.2 0.3 1.0
CB A:CYS26 3.2 0.5 1.0
CB A:CYS5 3.5 0.6 1.0
CB A:CYS8 3.5 0.4 1.0
N A:CYS8 3.6 0.6 1.0
N A:CYS26 3.9 0.3 1.0
CA A:CYS26 4.1 1.0 1.0
CA A:CYS8 4.1 0.6 1.0
N A:CYS29 4.4 0.3 1.0
CB A:LEU7 4.4 0.5 1.0
CA A:CYS29 4.4 0.3 1.0
C A:LEU7 4.5 0.8 1.0
C A:CYS8 4.7 0.2 1.0
CA A:LEU7 4.8 0.2 1.0
C A:CYS26 4.8 0.1 1.0
N A:LEU7 4.8 0.5 1.0
CB A:SER10 4.8 0.3 1.0
OG A:SER10 4.8 0.9 1.0
O A:CYS26 4.9 0.4 1.0
CA A:CYS5 4.9 0.7 1.0
N A:ASN9 4.9 0.7 1.0

Zinc binding site 4 out of 6 in 5rlq

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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 Z285782452


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 Z285782452 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:55.8
occ:1.00
 ND1 B:HIS39 2.1 60.0 1.0
NE2 B:HIS33 2.2 60.8 1.0
SG B:CYS16 2.2 69.4 1.0
SG B:CYS19 2.6 66.8 1.0
CE1 B:HIS39 3.1 60.9 1.0
CG B:HIS39 3.1 65.2 1.0
CE1 B:HIS33 3.1 60.5 1.0
CD2 B:HIS33 3.2 60.1 1.0
CB B:CYS16 3.4 73.6 1.0
CB B:HIS39 3.4 66.8 1.0
CB B:CYS19 3.4 69.5 1.0
N B:CYS19 3.4 72.5 1.0
CA B:CYS19 3.8 71.4 1.0
C B:ALA18 4.1 70.9 1.0
NE2 B:HIS39 4.2 63.4 1.0
CD2 B:HIS39 4.2 64.3 1.0
ND1 B:HIS33 4.3 58.5 1.0
CG B:HIS33 4.3 60.2 1.0
CB B:ALA18 4.4 65.9 1.0
CB B:ALA110 4.6 53.9 1.0
CA B:ALA18 4.6 69.9 1.0
CA B:CYS16 4.7 71.7 1.0
N B:ALA18 4.7 70.0 1.0
O B:ALA18 4.8 73.0 1.0
CA B:HIS39 4.9 66.4 1.0

Zinc binding site 5 out of 6 in 5rlq

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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 Z285782452


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 Z285782452 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:89.8
occ:1.00
 SG B:CYS5 2.2 80.4 1.0
SG B:CYS26 2.3 94.4 1.0
SG B:CYS29 2.6 81.2 1.0
CB B:CYS8 2.8 95.6 1.0
CB B:CYS29 3.1 75.7 1.0
CB B:CYS26 3.2 92.2 1.0
CB B:CYS5 3.3 90.9 1.0
SG B:CYS8 3.4 0.0 1.0
N B:CYS26 3.6 87.8 1.0
N B:CYS8 3.7 95.0 1.0
CA B:CYS8 3.9 94.3 1.0
CA B:CYS26 4.0 89.4 1.0
N B:CYS29 4.2 80.3 1.0
CA B:CYS29 4.3 76.3 1.0
OG B:SER10 4.6 96.2 1.0
CB B:SER10 4.6 98.5 1.0
C B:LEU7 4.6 90.7 1.0
CB B:LEU7 4.6 84.8 1.0
CA B:CYS5 4.7 88.2 1.0
N B:GLY99 4.8 98.9 1.0
C B:LEU25 4.8 83.1 1.0
C B:CYS8 4.8 93.7 1.0
C B:CYS26 4.8 89.0 1.0
N B:LEU7 4.9 84.9 1.0
N B:ASN9 4.9 98.1 1.0
CA B:LEU7 4.9 86.9 1.0
N B:SER10 5.0 97.7 1.0
CA B:GLY99 5.0 97.6 1.0

Zinc binding site 6 out of 6 in 5rlq

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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 Z285782452


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 Z285782452 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:1.0
occ:1.00
 SG B:CYS50 2.2 0.3 1.0
SG B:CYS55 2.4 0.1 1.0
ND1 B:HIS75 2.6 0.3 1.0
SG B:CYS72 2.9 0.9 1.0
CB B:CYS50 3.2 0.2 1.0
CB B:CYS55 3.4 0.3 1.0
CG B:HIS75 3.4 0.5 1.0
CB B:CYS72 3.5 0.5 1.0
CE1 B:HIS75 3.6 0.3 1.0
CB B:HIS75 3.6 0.8 1.0
N B:CYS72 3.8 0.5 1.0
CB B:ALA52 4.0 0.4 1.0
CA B:CYS72 4.2 0.7 1.0
CG2 B:VAL57 4.4 0.7 1.0
N B:HIS75 4.5 0.9 1.0
CD2 B:HIS75 4.6 0.3 1.0
CA B:CYS50 4.6 0.1 1.0
NE2 B:HIS75 4.6 0.1 1.0
CA B:HIS75 4.7 0.2 1.0
CB B:VAL57 4.7 0.6 1.0
CA B:CYS55 4.8 0.3 1.0
C B:TYR71 4.9 0.4 1.0
C B:CYS72 5.0 0.1 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: Wed Dec 16 07:21:16 2020

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