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Zinc in PDB 5rli: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795:
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 Z45617795, PDB code: 5rli 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) 81.01 / 2.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.846, 70.009, 84.938, 102.88, 95.84, 112.37
R / Rfree (%) 19.7 / 26.8

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 Z45617795 (pdb code 5rli). 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 Z45617795, PDB code: 5rli:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rli

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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 Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:54.5
occ:1.00
 SG A:CYS55 2.2 54.9 1.0
SG A:CYS50 2.3 51.8 1.0
ND1 A:HIS75 2.3 41.5 1.0
SG A:CYS72 2.5 56.6 1.0
CB A:CYS50 3.2 57.1 1.0
CE1 A:HIS75 3.3 46.8 1.0
CB A:CYS55 3.3 54.4 1.0
CG A:HIS75 3.3 39.7 1.0
CB A:CYS72 3.4 58.9 1.0
CB A:HIS75 3.5 43.6 1.0
N A:CYS72 3.8 51.0 1.0
CA A:CYS72 4.2 59.0 1.0
CB A:ALA52 4.2 55.5 1.0
NE2 A:HIS75 4.4 43.3 1.0
CD2 A:HIS75 4.4 39.9 1.0
CG2 A:VAL57 4.6 55.9 1.0
CA A:CYS50 4.7 52.5 1.0
CA A:CYS55 4.7 58.3 1.0
N A:HIS75 4.7 51.5 1.0
CB A:VAL57 4.7 55.8 1.0
CA A:HIS75 4.7 43.5 1.0
C A:TYR71 4.9 45.1 1.0
C A:CYS72 4.9 64.0 1.0

Zinc binding site 2 out of 6 in 5rli

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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 Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:48.3
occ:1.00
 NE2 A:HIS33 1.8 30.8 1.0
ND1 A:HIS39 2.1 67.0 1.0
SG A:CYS16 2.3 74.0 1.0
SG A:CYS19 2.5 48.1 1.0
CE1 A:HIS33 2.7 34.5 1.0
CD2 A:HIS33 2.9 38.0 1.0
N A:CYS19 3.1 42.4 1.0
CE1 A:HIS39 3.1 72.9 1.0
CG A:HIS39 3.1 67.6 1.0
CB A:CYS16 3.3 67.9 1.0
CB A:HIS39 3.4 61.5 1.0
CB A:CYS19 3.4 40.1 1.0
CA A:CYS19 3.6 45.1 1.0
ND1 A:HIS33 3.9 38.9 1.0
CG A:HIS33 4.0 41.1 1.0
C A:ALA18 4.1 58.8 1.0
CB A:ALA18 4.2 63.6 1.0
NE2 A:HIS39 4.2 67.9 1.0
CD2 A:HIS39 4.2 74.0 1.0
CB A:ALA110 4.4 57.7 1.0
CA A:ALA18 4.5 64.5 1.0
CA A:CYS16 4.7 64.3 1.0
N A:ALA18 4.7 59.0 1.0
CA A:HIS39 4.8 57.2 1.0
CE2 A:PHE106 4.9 43.7 1.0

Zinc binding site 3 out of 6 in 5rli

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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 Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:83.6
occ:1.00
 SG A:CYS5 2.0 69.8 1.0
SG A:CYS8 2.4 88.4 1.0
SG A:CYS29 2.4 69.0 1.0
SG A:CYS26 2.7 63.7 1.0
CB A:CYS29 3.0 76.7 1.0
CB A:CYS26 3.1 65.0 1.0
CB A:CYS5 3.2 77.5 1.0
CB A:CYS8 3.6 88.0 1.0
N A:CYS26 3.7 66.8 1.0
N A:CYS8 3.9 86.2 1.0
CA A:CYS26 4.0 67.8 1.0
CA A:CYS8 4.2 86.1 1.0
CA A:CYS29 4.3 75.2 1.0
CB A:LEU7 4.4 75.5 1.0
N A:CYS29 4.4 76.1 1.0
O A:CYS26 4.6 80.0 1.0
CA A:CYS5 4.6 84.8 1.0
C A:CYS26 4.7 76.7 1.0
C A:CYS8 4.8 84.1 1.0
N A:ASN9 4.8 87.2 1.0
C A:LEU7 4.8 82.1 1.0
C A:CYS5 4.9 89.3 1.0
N A:LEU7 4.9 71.9 1.0
CB A:SER10 4.9 71.4 1.0
C A:LEU25 4.9 68.6 1.0
O A:CYS5 4.9 81.3 1.0
CA A:LEU7 5.0 78.8 1.0

Zinc binding site 4 out of 6 in 5rli

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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 Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:36.9
occ:1.00
 NE2 B:HIS33 1.9 29.9 1.0
ND1 B:HIS39 2.1 46.3 1.0
SG B:CYS16 2.2 41.3 1.0
SG B:CYS19 2.3 37.3 1.0
CD2 B:HIS33 2.9 33.3 1.0
CE1 B:HIS33 2.9 30.6 1.0
CG B:HIS39 3.1 48.7 1.0
CE1 B:HIS39 3.1 47.0 1.0
CB B:HIS39 3.3 46.2 1.0
CB B:CYS19 3.3 35.1 1.0
CB B:CYS16 3.3 40.4 1.0
N B:CYS19 3.3 45.9 1.0
CA B:CYS19 3.7 42.4 1.0
ND1 B:HIS33 4.0 30.0 1.0
CG B:HIS33 4.0 32.4 1.0
C B:ALA18 4.2 46.5 1.0
CD2 B:HIS39 4.2 45.7 1.0
NE2 B:HIS39 4.2 49.4 1.0
CB B:ALA110 4.5 35.0 1.0
CB B:ALA18 4.6 40.7 1.0
CA B:CYS16 4.7 39.2 1.0
CA B:ALA18 4.8 44.7 1.0
CA B:HIS39 4.8 42.9 1.0
N B:ALA18 4.9 44.7 1.0
O B:ALA18 4.9 43.8 1.0

Zinc binding site 5 out of 6 in 5rli

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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 Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:49.4
occ:1.00
 SG B:CYS29 2.2 47.4 1.0
SG B:CYS26 2.3 50.6 1.0
SG B:CYS5 2.4 53.7 1.0
CB B:CYS8 2.8 69.0 1.0
CB B:CYS29 3.0 47.4 1.0
SG B:CYS8 3.2 88.0 1.0
CB B:CYS5 3.4 60.3 1.0
CB B:CYS26 3.5 52.0 1.0
N B:CYS8 3.7 71.2 1.0
CA B:CYS8 3.8 74.1 1.0
N B:CYS26 4.0 55.1 1.0
N B:CYS29 4.0 50.2 1.0
CA B:CYS29 4.1 44.9 1.0
CA B:CYS26 4.3 52.9 1.0
CB B:LEU7 4.4 71.9 1.0
OG B:SER10 4.5 63.5 1.0
CB B:SER10 4.5 63.1 1.0
CA B:GLY99 4.6 62.7 1.0
N B:GLY99 4.6 63.5 1.0
C B:LEU7 4.6 72.7 1.0
CA B:CYS5 4.9 61.6 1.0
C B:CYS8 4.9 67.5 1.0
C B:CYS26 4.9 54.6 1.0
CA B:LEU7 5.0 70.2 1.0

Zinc binding site 6 out of 6 in 5rli

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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 Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:62.1
occ:1.00
 SG B:CYS50 2.2 60.4 1.0
SG B:CYS55 2.3 65.5 1.0
ND1 B:HIS75 2.4 73.8 1.0
SG B:CYS72 2.6 54.2 1.0
CB B:CYS50 3.1 62.0 1.0
CB B:CYS55 3.2 74.1 1.0
CG B:HIS75 3.3 74.2 1.0
CB B:HIS75 3.4 65.1 1.0
CE1 B:HIS75 3.4 73.5 1.0
CB B:CYS72 3.5 59.5 1.0
N B:CYS72 3.8 52.7 1.0
CB B:ALA52 4.1 77.0 1.0
CA B:CYS72 4.2 60.2 1.0
CG2 B:VAL57 4.3 78.1 1.0
CD2 B:HIS75 4.5 78.1 1.0
N B:HIS75 4.5 56.2 1.0
NE2 B:HIS75 4.5 76.0 1.0
CA B:CYS50 4.5 63.2 1.0
CA B:HIS75 4.6 61.5 1.0
CA B:CYS55 4.6 78.1 1.0
CB B:VAL57 4.7 78.3 1.0
C B:CYS72 4.9 64.7 1.0
C B:TYR71 4.9 54.6 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 04:00:42 2024

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