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Zinc in PDB 5rlj: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1407673036

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1407673036

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1407673036:
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 Z1407673036, PDB code: 5rlj 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) 81.47 / 1.88
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.146, 70.207, 85.329, 102.49, 96.07, 112.49
R / Rfree (%) 17.3 / 22.8

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 Z1407673036 (pdb code 5rlj). 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 Z1407673036, PDB code: 5rlj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlj

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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 Z1407673036


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 Z1407673036 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:64.3
occ:1.00
 SG A:CYS55 2.3 65.6 1.0
SG A:CYS50 2.3 66.3 1.0
ND1 A:HIS75 2.4 56.2 1.0
SG A:CYS72 2.7 65.0 1.0
CB A:CYS50 3.1 65.6 1.0
CB A:CYS55 3.1 67.5 1.0
CE1 A:HIS75 3.3 55.9 1.0
CG A:HIS75 3.4 55.2 1.0
CB A:CYS72 3.4 61.3 1.0
CB A:HIS75 3.6 54.8 1.0
N A:CYS72 3.8 57.9 1.0
CA A:CYS72 4.2 59.2 1.0
CB A:ALA52 4.2 59.0 1.0
NE2 A:HIS75 4.5 55.4 1.0
CG2 A:VAL57 4.5 67.1 1.0
CD2 A:HIS75 4.5 54.8 1.0
N A:HIS75 4.5 59.4 1.0
CA A:CYS50 4.5 65.5 1.0
CA A:CYS55 4.6 69.5 1.0
CB A:VAL57 4.6 69.2 1.0
CA A:HIS75 4.7 57.3 1.0
C A:TYR71 4.9 55.8 1.0
C A:CYS72 4.9 62.2 1.0

Zinc binding site 2 out of 6 in 5rlj

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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 Z1407673036


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 Z1407673036 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:60.3
occ:1.00
 NE2 A:HIS33 2.0 50.9 1.0
ND1 A:HIS39 2.1 67.9 1.0
SG A:CYS16 2.3 69.3 1.0
SG A:CYS19 2.3 60.4 1.0
CE1 A:HIS33 3.0 55.2 1.0
CD2 A:HIS33 3.0 56.1 1.0
CG A:HIS39 3.1 67.9 1.0
CE1 A:HIS39 3.1 67.4 1.0
CB A:CYS16 3.3 67.6 1.0
CB A:HIS39 3.4 64.6 1.0
CB A:CYS19 3.5 57.0 1.0
N A:CYS19 3.5 63.8 1.0
CA A:CYS19 3.8 61.9 1.0
ND1 A:HIS33 4.1 56.8 1.0
CG A:HIS33 4.1 58.0 1.0
C A:ALA18 4.2 66.2 1.0
NE2 A:HIS39 4.2 69.2 1.0
CD2 A:HIS39 4.2 67.9 1.0
CB A:ALA110 4.4 52.0 1.0
CB A:ALA18 4.5 65.7 1.0
CA A:CYS16 4.7 71.0 1.0
CA A:ALA18 4.7 64.7 1.0
N A:ALA18 4.8 65.7 1.0
CE2 A:PHE106 4.8 62.1 1.0
CA A:HIS39 4.9 64.5 1.0
O A:ALA18 4.9 67.6 1.0
CZ A:PHE106 5.0 61.0 1.0

Zinc binding site 3 out of 6 in 5rlj

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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 Z1407673036


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 Z1407673036 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.1
occ:1.00
 SG A:CYS29 2.2 0.7 1.0
SG A:CYS5 2.4 90.5 1.0
SG A:CYS26 2.5 85.8 1.0
SG A:CYS8 2.6 0.1 1.0
CB A:CYS29 3.1 94.5 1.0
CB A:CYS5 3.4 89.6 1.0
CB A:CYS8 3.5 0.3 1.0
N A:CYS8 3.5 0.4 1.0
CB A:CYS26 3.6 86.3 1.0
CA A:CYS8 3.9 0.9 1.0
N A:CYS26 4.1 85.4 1.0
CB A:LEU7 4.1 94.2 1.0
C A:LEU7 4.3 0.1 1.0
CA A:CYS26 4.4 88.0 1.0
CA A:CYS29 4.4 86.8 1.0
N A:CYS29 4.5 89.6 1.0
C A:CYS8 4.6 0.6 1.0
CA A:LEU7 4.6 93.3 1.0
N A:LEU7 4.7 92.1 1.0
CB A:SER10 4.7 0.5 1.0
O A:CYS26 4.7 85.9 1.0
N A:ASN9 4.8 0.2 1.0
CA A:CYS5 4.8 89.2 1.0
OG A:SER10 4.9 0.8 1.0
C A:CYS26 4.9 88.1 1.0
N A:SER10 5.0 0.2 1.0

Zinc binding site 4 out of 6 in 5rlj

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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 Z1407673036


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 Z1407673036 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:46.6
occ:1.00
 NE2 B:HIS33 2.0 49.3 1.0
ND1 B:HIS39 2.1 48.8 1.0
SG B:CYS16 2.2 50.0 1.0
SG B:CYS19 2.4 49.4 1.0
CD2 B:HIS33 3.0 48.7 1.0
CE1 B:HIS33 3.0 48.5 1.0
CG B:HIS39 3.1 51.0 1.0
CE1 B:HIS39 3.1 50.2 1.0
CB B:CYS16 3.2 53.6 1.0
CB B:HIS39 3.3 50.8 1.0
CB B:CYS19 3.5 49.2 1.0
N B:CYS19 3.5 50.4 1.0
CA B:CYS19 3.8 49.0 1.0
CG B:HIS33 4.1 49.1 1.0
ND1 B:HIS33 4.1 47.7 1.0
C B:ALA18 4.2 50.7 1.0
CD2 B:HIS39 4.2 50.4 1.0
NE2 B:HIS39 4.2 50.0 1.0
CB B:ALA18 4.5 47.5 1.0
CB B:ALA110 4.5 41.2 1.0
CA B:CYS16 4.6 55.3 1.0
CA B:ALA18 4.7 49.6 1.0
N B:ALA18 4.8 51.6 1.0
CA B:HIS39 4.8 51.8 1.0
O B:ALA18 4.9 51.6 1.0
CE2 B:PHE106 5.0 44.3 1.0
C B:CYS16 5.0 55.8 1.0

Zinc binding site 5 out of 6 in 5rlj

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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 Z1407673036


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 Z1407673036 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:77.0
occ:1.00
 SG B:CYS26 2.2 63.3 1.0
SG B:CYS5 2.4 64.3 1.0
SG B:CYS29 2.5 69.3 1.0
CB B:CYS8 2.7 77.0 1.0
CB B:CYS29 3.0 59.9 1.0
SG B:CYS8 3.2 83.5 1.0
CB B:CYS5 3.5 71.1 1.0
CB B:CYS26 3.6 64.5 1.0
N B:CYS8 3.8 75.3 1.0
N B:CYS26 3.9 63.4 1.0
CA B:CYS8 3.9 77.2 1.0
N B:CYS29 3.9 56.5 1.0
CA B:CYS29 4.1 54.7 1.0
CA B:CYS26 4.3 64.0 1.0
CB B:LEU7 4.5 71.7 1.0
C B:LEU7 4.6 72.3 1.0
N B:GLY99 4.7 86.7 1.0
CA B:GLY99 4.7 84.2 1.0
CB B:SER10 4.7 72.0 1.0
OG B:SER10 4.9 65.5 1.0
CA B:CYS5 4.9 70.1 1.0
C B:CYS8 4.9 77.6 1.0
C B:CYS26 5.0 66.1 1.0
CA B:LEU7 5.0 71.0 1.0

Zinc binding site 6 out of 6 in 5rlj

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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 Z1407673036


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 Z1407673036 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:89.4
occ:1.00
 SG B:CYS50 2.2 92.2 1.0
SG B:CYS55 2.3 0.3 1.0
ND1 B:HIS75 2.5 89.6 1.0
SG B:CYS72 2.8 81.0 1.0
CB B:CYS50 2.9 96.9 1.0
CB B:CYS55 3.1 0.8 1.0
CG B:HIS75 3.5 87.8 1.0
CB B:CYS72 3.5 76.7 1.0
CE1 B:HIS75 3.5 89.5 1.0
CB B:HIS75 3.6 84.9 1.0
N B:CYS72 3.7 76.2 1.0
CA B:CYS72 4.2 77.0 1.0
CB B:ALA52 4.2 0.5 1.0
CA B:CYS50 4.4 95.0 1.0
CA B:CYS55 4.5 0.1 1.0
CG2 B:VAL57 4.5 98.8 1.0
N B:HIS75 4.6 81.3 1.0
CD2 B:HIS75 4.6 88.4 1.0
NE2 B:HIS75 4.6 89.0 1.0
CB B:VAL57 4.6 1.0 1.0
CA B:HIS75 4.8 82.4 1.0
C B:TYR71 4.8 75.6 1.0
C B:CYS50 5.0 99.8 1.0
C B:CYS72 5.0 80.7 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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