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Zinc in PDB 5rl9: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1703168683

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1703168683

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1703168683:
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 Z1703168683, PDB code: 5rl9 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) 81.49 / 1.79
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.119, 70.182, 85.413, 102.61, 96.08, 112.48
R / Rfree (%) 17.7 / 23.1

Other elements in 5rl9:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1703168683 also contains other interesting chemical elements:

Fluorine (F) 1 atom

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 Z1703168683 (pdb code 5rl9). 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 Z1703168683, PDB code: 5rl9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rl9

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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 Z1703168683


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 Z1703168683 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:59.7
occ:1.00
 SG A:CYS50 2.2 64.1 1.0
ND1 A:HIS75 2.4 55.5 1.0
SG A:CYS55 2.4 62.5 1.0
SG A:CYS72 2.7 62.3 1.0
CB A:CYS50 3.1 65.2 1.0
CB A:CYS55 3.3 67.2 1.0
CE1 A:HIS75 3.3 54.8 1.0
CG A:HIS75 3.4 54.4 1.0
CB A:CYS72 3.5 57.9 1.0
CB A:HIS75 3.6 53.3 1.0
N A:CYS72 3.8 56.6 1.0
CB A:ALA52 4.2 60.6 1.0
CA A:CYS72 4.2 57.4 1.0
N A:HIS75 4.5 58.7 1.0
CG2 A:VAL57 4.5 66.7 1.0
NE2 A:HIS75 4.5 54.8 1.0
CD2 A:HIS75 4.5 53.5 1.0
CA A:CYS50 4.5 64.8 1.0
CB A:VAL57 4.6 66.6 1.0
CA A:HIS75 4.7 56.6 1.0
CA A:CYS55 4.7 70.2 1.0
C A:TYR71 4.9 56.4 1.0
C A:CYS72 5.0 61.4 1.0

Zinc binding site 2 out of 6 in 5rl9

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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 Z1703168683


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 Z1703168683 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:58.8
occ:1.00
 NE2 A:HIS33 2.0 49.2 1.0
ND1 A:HIS39 2.0 66.8 1.0
SG A:CYS19 2.3 63.0 1.0
SG A:CYS16 2.3 72.1 1.0
CE1 A:HIS33 2.9 51.6 1.0
CE1 A:HIS39 3.0 66.5 1.0
CD2 A:HIS33 3.0 53.7 1.0
CG A:HIS39 3.1 67.2 1.0
CB A:CYS16 3.3 70.8 1.0
CB A:HIS39 3.4 65.0 1.0
CB A:CYS19 3.4 58.5 1.0
N A:CYS19 3.4 62.8 1.0
CA A:CYS19 3.7 62.2 1.0
ND1 A:HIS33 4.1 53.7 1.0
CG A:HIS33 4.1 55.3 1.0
C A:ALA18 4.2 67.2 1.0
NE2 A:HIS39 4.2 69.7 1.0
CD2 A:HIS39 4.2 67.6 1.0
CB A:ALA110 4.5 53.3 1.0
CB A:ALA18 4.5 66.3 1.0
CA A:ALA18 4.7 64.6 1.0
CA A:CYS16 4.7 71.2 1.0
N A:ALA18 4.8 65.8 1.0
CA A:HIS39 4.9 64.5 1.0
CE2 A:PHE106 4.9 62.3 1.0
O A:ALA18 4.9 68.3 1.0
C A:CYS16 5.0 68.7 1.0

Zinc binding site 3 out of 6 in 5rl9

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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 Z1703168683


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 Z1703168683 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:99.5
occ:1.00
 SG A:CYS29 2.4 91.9 1.0
SG A:CYS26 2.4 86.0 1.0
SG A:CYS8 2.5 98.1 1.0
SG A:CYS5 2.5 90.7 1.0
CB A:CYS29 3.2 86.8 1.0
CB A:CYS5 3.5 87.7 1.0
CB A:CYS26 3.6 83.5 1.0
CB A:CYS8 3.6 94.2 1.0
N A:CYS8 3.8 96.4 1.0
N A:CYS26 4.1 79.9 1.0
CA A:CYS8 4.2 97.2 1.0
CB A:LEU7 4.3 91.2 1.0
CA A:CYS26 4.3 84.8 1.0
CA A:CYS29 4.4 82.2 1.0
N A:CYS29 4.4 85.8 1.0
C A:LEU7 4.5 96.9 1.0
CB A:SER10 4.7 0.8 1.0
CA A:LEU7 4.7 91.5 1.0
C A:CYS8 4.8 99.5 1.0
N A:LEU7 4.8 89.2 1.0
O A:CYS26 4.9 85.4 1.0
CA A:CYS5 4.9 87.5 1.0
OG A:SER10 4.9 96.5 1.0
C A:CYS26 5.0 85.2 1.0

Zinc binding site 4 out of 6 in 5rl9

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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 Z1703168683


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 Z1703168683 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:46.9
occ:1.00
 NE2 B:HIS33 2.0 49.7 1.0
ND1 B:HIS39 2.1 42.3 1.0
SG B:CYS16 2.2 53.1 1.0
SG B:CYS19 2.4 49.5 1.0
CD2 B:HIS33 3.0 48.4 1.0
CE1 B:HIS33 3.0 48.0 1.0
CG B:HIS39 3.1 45.8 1.0
CE1 B:HIS39 3.1 43.2 1.0
CB B:CYS16 3.3 54.5 1.0
CB B:HIS39 3.3 45.5 1.0
CB B:CYS19 3.4 48.8 1.0
N B:CYS19 3.4 49.6 1.0
CA B:CYS19 3.7 48.9 1.0
CG B:HIS33 4.1 49.0 1.0
ND1 B:HIS33 4.1 46.5 1.0
C B:ALA18 4.2 49.6 1.0
CD2 B:HIS39 4.2 44.7 1.0
NE2 B:HIS39 4.3 44.0 1.0
CB B:ALA18 4.5 46.3 1.0
CB B:ALA110 4.6 42.7 1.0
CA B:CYS16 4.7 55.6 1.0
CA B:ALA18 4.7 48.9 1.0
N B:ALA18 4.7 51.6 1.0
CA B:HIS39 4.8 47.2 1.0
C B:CYS16 4.9 55.9 1.0
O B:ALA18 5.0 50.1 1.0

Zinc binding site 5 out of 6 in 5rl9

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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 Z1703168683


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 Z1703168683 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:74.7
occ:1.00
 SG B:CYS26 2.3 69.8 1.0
SG B:CYS5 2.4 68.3 1.0
SG B:CYS29 2.5 72.8 1.0
CB B:CYS8 2.9 85.0 1.0
CB B:CYS29 3.0 63.0 1.0
SG B:CYS8 3.1 90.5 1.0
CB B:CYS26 3.5 68.2 1.0
CB B:CYS5 3.5 74.8 1.0
N B:CYS26 3.8 65.5 1.0
N B:CYS29 3.9 57.3 1.0
N B:CYS8 3.9 84.1 1.0
CA B:CYS8 4.1 83.5 1.0
CA B:CYS29 4.1 56.6 1.0
CA B:CYS26 4.2 66.2 1.0
CB B:LEU7 4.6 81.8 1.0
C B:LEU7 4.7 81.4 1.0
O B:CYS26 4.7 67.6 1.0
CB B:SER10 4.7 79.8 1.0
C B:CYS26 4.8 67.6 1.0
N B:GLY99 4.8 87.8 1.0
CA B:GLY99 4.8 86.3 1.0
OG B:SER10 4.9 73.5 1.0
CA B:CYS5 4.9 75.2 1.0
C B:LEU25 5.0 64.4 1.0

Zinc binding site 6 out of 6 in 5rl9

Go back to Zinc Binding Sites List in 5rl9
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1703168683


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 Z1703168683 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:93.7
occ:1.00
 SG B:CYS50 2.2 78.4 1.0
SG B:CYS55 2.3 0.3 1.0
ND1 B:HIS75 2.5 88.3 1.0
SG B:CYS72 2.7 79.3 1.0
CB B:CYS50 3.0 84.0 1.0
CB B:CYS55 3.2 0.3 1.0
CE1 B:HIS75 3.4 89.1 1.0
CB B:CYS72 3.5 75.3 1.0
CG B:HIS75 3.5 86.5 1.0
CB B:HIS75 3.7 82.8 1.0
N B:CYS72 3.8 74.2 1.0
CA B:CYS72 4.2 74.7 1.0
CB B:ALA52 4.3 0.3 1.0
CG2 B:VAL57 4.4 88.8 1.0
CA B:CYS50 4.5 84.1 1.0
CB B:VAL57 4.5 91.0 1.0
N B:HIS75 4.6 79.8 1.0
NE2 B:HIS75 4.6 90.7 1.0
CA B:CYS55 4.6 0.1 1.0
CD2 B:HIS75 4.6 89.5 1.0
CA B:HIS75 4.8 81.0 1.0
C B:TYR71 4.9 73.6 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 03:54:46 2024

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