Zinc in PDB 5rlg: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19739650

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19739650

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z19739650:
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 Z19739650, PDB code: 5rlg 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) 81.54 / 1.96
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.184, 70.314, 85.682, 103.01, 96.26, 112.07
R / Rfree (%) 24.6 / 28.6

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 Z19739650 (pdb code 5rlg). 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 Z19739650, PDB code: 5rlg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlg

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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 Z19739650


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 Z19739650 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:42.7
occ:1.00
 SG B:CYS16 2.1 45.3 1.0
ND1 B:HIS39 2.1 42.5 1.0
SG B:CYS19 2.3 43.4 1.0
NE2 B:HIS33 2.4 36.8 1.0
CE1 B:HIS39 3.1 45.2 1.0
CG B:HIS39 3.1 47.9 1.0
CB B:CYS16 3.1 52.3 1.0
CB B:CYS19 3.2 37.5 1.0
CD2 B:HIS33 3.3 34.8 1.0
N B:CYS19 3.3 48.0 1.0
CB B:HIS39 3.4 48.5 1.0
CE1 B:HIS33 3.5 40.8 1.0
CA B:CYS19 3.6 42.6 1.0
NE2 B:HIS39 4.2 46.2 1.0
CD2 B:HIS39 4.2 48.3 1.0
C B:ALA18 4.2 47.4 1.0
CG B:HIS33 4.5 38.1 1.0
CB B:ALA18 4.5 45.2 1.0
CA B:CYS16 4.5 53.5 1.0
ND1 B:HIS33 4.5 41.1 1.0
CB B:ALA110 4.7 41.5 1.0
CA B:ALA18 4.7 45.4 1.0
N B:ALA18 4.7 49.2 1.0
CA B:HIS39 4.8 43.1 1.0
C B:CYS16 4.9 51.9 1.0

Zinc binding site 2 out of 6 in 5rlg

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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 Z19739650


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 Z19739650 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:59.8
occ:1.00
 SG B:CYS5 1.9 90.4 1.0
SG B:CYS29 2.4 67.5 1.0
SG B:CYS26 2.4 91.3 1.0
CB B:CYS29 2.9 59.9 1.0
CB B:CYS26 2.9 67.3 1.0
CB B:CYS5 3.2 93.5 1.0
CB B:CYS8 3.2 92.1 1.0
SG B:CYS8 3.4 94.7 1.0
N B:CYS26 3.5 80.2 1.0
CA B:CYS26 3.7 79.3 1.0
N B:CYS8 3.9 0.3 1.0
N B:CYS29 4.0 60.0 1.0
CA B:CYS29 4.0 56.4 1.0
CA B:CYS8 4.1 96.9 1.0
O B:CYS26 4.2 88.5 1.0
C B:CYS26 4.3 81.7 1.0
CA B:CYS5 4.5 90.0 1.0
CB B:SER10 4.6 78.0 1.0
CB B:LEU7 4.7 98.9 1.0
N B:GLY99 4.7 75.1 1.0
CA B:GLY99 4.7 68.4 1.0
C B:LEU25 4.7 72.8 1.0
C B:LEU7 4.9 96.0 1.0

Zinc binding site 3 out of 6 in 5rlg

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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 Z19739650


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 Z19739650 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:76.4
occ:1.00
 ND1 B:HIS75 2.3 86.2 1.0
SG B:CYS55 2.4 77.3 1.0
SG B:CYS50 2.5 79.9 1.0
SG B:CYS72 2.8 66.1 1.0
CB B:CYS55 2.9 90.2 1.0
CE1 B:HIS75 3.0 86.7 1.0
CG B:HIS75 3.3 81.6 1.0
CB B:CYS50 3.4 84.4 1.0
CB B:CYS72 3.6 64.1 1.0
CB B:HIS75 3.8 76.5 1.0
CB B:ALA52 4.0 99.8 1.0
N B:CYS72 4.0 57.9 1.0
NE2 B:HIS75 4.1 87.5 1.0
CD2 B:HIS75 4.2 87.4 1.0
CG2 B:VAL57 4.3 86.9 1.0
CA B:CYS55 4.4 94.8 1.0
CA B:CYS72 4.4 64.8 1.0
CB B:VAL57 4.6 92.3 1.0
N B:HIS75 4.8 66.1 1.0
CA B:CYS50 4.8 83.3 1.0
CA B:HIS75 4.9 74.5 1.0
C B:CYS55 4.9 96.7 1.0

Zinc binding site 4 out of 6 in 5rlg

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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 Z19739650


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 Z19739650 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:53.2
occ:1.00
 ND1 A:HIS75 2.2 50.7 1.0
SG A:CYS55 2.2 58.7 1.0
SG A:CYS50 2.4 48.0 1.0
SG A:CYS72 2.6 57.8 1.0
CE1 A:HIS75 3.0 49.3 1.0
CB A:CYS55 3.2 54.4 1.0
CG A:HIS75 3.3 48.7 1.0
CB A:CYS72 3.3 55.5 1.0
CB A:CYS50 3.3 53.0 1.0
CB A:HIS75 3.7 48.4 1.0
N A:CYS72 3.9 52.3 1.0
CA A:CYS72 4.1 57.0 1.0
NE2 A:HIS75 4.2 44.2 1.0
CB A:ALA52 4.3 53.7 1.0
CD2 A:HIS75 4.3 47.0 1.0
CG2 A:VAL57 4.6 60.9 1.0
CA A:CYS55 4.6 59.7 1.0
CA A:CYS50 4.7 54.3 1.0
C A:CYS72 4.7 63.0 1.0
CB A:VAL57 4.8 61.0 1.0
N A:HIS75 4.8 47.3 1.0
O A:CYS72 4.8 65.7 1.0
CA A:HIS75 4.9 46.8 1.0
CB A:SER74 4.9 56.1 1.0

Zinc binding site 5 out of 6 in 5rlg

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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 Z19739650


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 Z19739650 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:48.6
occ:1.00
 NE2 A:HIS33 1.7 26.7 1.0
ND1 A:HIS39 2.1 69.3 1.0
SG A:CYS16 2.3 62.6 1.0
SG A:CYS19 2.5 50.3 1.0
CE1 A:HIS33 2.6 32.2 1.0
CD2 A:HIS33 2.8 36.4 1.0
CE1 A:HIS39 3.0 69.7 1.0
CG A:HIS39 3.0 72.6 1.0
N A:CYS19 3.3 54.1 1.0
CB A:HIS39 3.3 62.0 1.0
CB A:CYS16 3.4 71.8 1.0
CB A:CYS19 3.7 42.0 1.0
ND1 A:HIS33 3.7 38.4 1.0
CG A:HIS33 3.8 39.8 1.0
CA A:CYS19 3.9 49.3 1.0
CB A:ALA18 4.1 75.0 1.0
C A:ALA18 4.1 67.6 1.0
NE2 A:HIS39 4.1 76.5 1.0
CD2 A:HIS39 4.1 77.9 1.0
CB A:ALA110 4.4 60.1 1.0
CA A:ALA18 4.5 73.8 1.0
N A:ALA18 4.8 69.2 1.0
CA A:CYS16 4.8 72.7 1.0
CA A:HIS39 4.8 59.9 1.0
CE2 A:PHE106 4.9 49.0 1.0
CZ A:PHE106 4.9 49.8 1.0

Zinc binding site 6 out of 6 in 5rlg

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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 Z19739650


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 Z19739650 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:96.9
occ:1.00
 SG A:CYS26 2.3 0.8 1.0
SG A:CYS5 2.4 97.7 1.0
SG A:CYS8 2.6 0.2 1.0
SG A:CYS29 2.6 79.4 1.0
CB A:CYS26 3.1 0.5 1.0
CB A:CYS29 3.2 89.1 1.0
CB A:CYS8 3.3 0.6 1.0
CB A:CYS5 3.6 98.5 1.0
N A:CYS8 3.8 1.0 1.0
N A:CYS26 3.9 97.8 1.0
CA A:CYS26 4.0 99.9 1.0
CA A:CYS8 4.1 0.1 1.0
CB A:LEU7 4.3 0.6 1.0
CA A:CYS29 4.5 89.3 1.0
N A:CYS29 4.5 93.3 1.0
O A:CYS26 4.6 96.2 1.0
C A:CYS26 4.7 99.4 1.0
C A:LEU7 4.7 0.8 1.0
C A:CYS8 4.9 0.6 1.0
CA A:LEU7 4.9 0.8 1.0
CA A:CYS5 5.0 97.5 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: Mon Oct 28 04:00:42 2024

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