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Zinc in PDB 5rlc: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z56923284

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z56923284

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z56923284:
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 Z56923284, PDB code: 5rlc 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) 81.30 / 1.92
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.228, 70.191, 85.166, 102.63, 95.94, 112.44
R / Rfree (%) 20.6 / 25.2

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 Z56923284 (pdb code 5rlc). 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 Z56923284, PDB code: 5rlc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlc

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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 Z56923284


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 Z56923284 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:55.8
occ:1.00
 SG A:CYS55 2.2 56.4 1.0
SG A:CYS50 2.2 51.1 1.0
ND1 A:HIS75 2.2 50.5 1.0
SG A:CYS72 2.5 61.0 1.0
CE1 A:HIS75 3.1 49.8 1.0
CB A:CYS50 3.1 55.1 1.0
CB A:CYS55 3.2 56.9 1.0
CG A:HIS75 3.2 46.8 1.0
CB A:CYS72 3.3 56.9 1.0
CB A:HIS75 3.6 48.1 1.0
N A:CYS72 3.9 54.0 1.0
CA A:CYS72 4.2 56.2 1.0
NE2 A:HIS75 4.3 47.0 1.0
CB A:ALA52 4.3 56.3 1.0
CD2 A:HIS75 4.3 46.0 1.0
CA A:CYS50 4.5 52.3 1.0
CA A:CYS55 4.6 59.7 1.0
N A:HIS75 4.6 54.5 1.0
CA A:HIS75 4.7 50.6 1.0
CB A:VAL57 4.8 53.0 1.0
CG2 A:VAL57 4.8 52.5 1.0
C A:CYS72 4.9 62.1 1.0
CB A:SER74 5.0 56.9 1.0
C A:TYR71 5.0 48.0 1.0

Zinc binding site 2 out of 6 in 5rlc

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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 Z56923284


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 Z56923284 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:49.9
occ:1.00
 NE2 A:HIS33 1.8 32.6 1.0
ND1 A:HIS39 2.0 58.1 1.0
SG A:CYS16 2.2 65.4 1.0
SG A:CYS19 2.3 56.0 1.0
CE1 A:HIS33 2.7 40.5 1.0
CD2 A:HIS33 2.9 41.4 1.0
CE1 A:HIS39 3.0 60.5 1.0
CG A:HIS39 3.0 63.5 1.0
N A:CYS19 3.1 55.5 1.0
CB A:CYS16 3.3 62.6 1.0
CB A:HIS39 3.3 57.4 1.0
CB A:CYS19 3.4 43.9 1.0
CA A:CYS19 3.7 50.0 1.0
ND1 A:HIS33 3.9 41.1 1.0
CG A:HIS33 4.0 42.6 1.0
CB A:ALA18 4.0 66.0 1.0
NE2 A:HIS39 4.1 64.6 1.0
CD2 A:HIS39 4.1 65.1 1.0
C A:ALA18 4.1 58.6 1.0
CB A:ALA110 4.4 56.4 1.0
CA A:ALA18 4.5 63.5 1.0
N A:ALA18 4.7 54.5 1.0
CA A:CYS16 4.7 61.5 1.0
CA A:HIS39 4.8 54.7 1.0
CE2 A:PHE106 4.8 51.0 1.0
CZ A:PHE106 4.9 51.9 1.0

Zinc binding site 3 out of 6 in 5rlc

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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 Z56923284


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 Z56923284 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:75.8
occ:1.00
 SG A:CYS29 2.2 61.6 1.0
SG A:CYS5 2.3 83.3 1.0
SG A:CYS26 2.5 74.8 1.0
SG A:CYS8 2.6 87.2 1.0
CB A:CYS29 3.0 68.3 1.0
CB A:CYS26 3.1 67.7 1.0
CB A:CYS5 3.4 87.8 1.0
CB A:CYS8 3.5 91.1 1.0
N A:CYS26 3.7 65.4 1.0
CA A:CYS26 3.9 66.4 1.0
N A:CYS8 4.0 90.0 1.0
N A:CYS29 4.2 69.0 1.0
CA A:CYS29 4.2 69.5 1.0
O A:CYS26 4.3 65.6 1.0
CA A:CYS8 4.3 95.3 1.0
CB A:LEU7 4.3 87.3 1.0
C A:CYS26 4.5 74.0 1.0
CA A:CYS5 4.7 87.3 1.0
C A:LEU7 4.8 85.7 1.0
CB A:SER10 4.8 85.5 1.0
CA A:LEU7 4.9 85.9 1.0
C A:LEU25 4.9 67.5 1.0
N A:ASN9 5.0 91.5 1.0
N A:LEU7 5.0 80.5 1.0
C A:CYS8 5.0 95.9 1.0

Zinc binding site 4 out of 6 in 5rlc

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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 Z56923284


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 Z56923284 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:41.4
occ:1.00
 NE2 B:HIS33 1.9 32.1 1.0
ND1 B:HIS39 2.0 50.2 1.0
SG B:CYS16 2.2 46.6 1.0
SG B:CYS19 2.4 43.4 1.0
CD2 B:HIS33 2.8 33.3 1.0
CE1 B:HIS33 3.0 37.4 1.0
CG B:HIS39 3.0 52.4 1.0
CE1 B:HIS39 3.0 53.0 1.0
CB B:HIS39 3.3 49.4 1.0
CB B:CYS16 3.3 52.8 1.0
N B:CYS19 3.4 51.1 1.0
CB B:CYS19 3.4 37.5 1.0
CA B:CYS19 3.8 44.1 1.0
CG B:HIS33 4.0 35.2 1.0
ND1 B:HIS33 4.0 34.7 1.0
CD2 B:HIS39 4.1 51.4 1.0
NE2 B:HIS39 4.1 51.3 1.0
C B:ALA18 4.4 52.0 1.0
CB B:ALA110 4.5 38.8 1.0
CB B:ALA18 4.6 43.5 1.0
CA B:CYS16 4.7 54.0 1.0
CA B:HIS39 4.8 46.4 1.0
N B:ALA18 4.8 46.1 1.0
CA B:ALA18 4.8 48.1 1.0
CE2 B:PHE106 4.8 37.8 1.0
C B:CYS16 4.9 52.1 1.0
CZ B:PHE106 5.0 41.5 1.0

Zinc binding site 5 out of 6 in 5rlc

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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 Z56923284


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 Z56923284 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:64.4
occ:1.00
 SG B:CYS29 2.1 55.0 1.0
SG B:CYS5 2.2 64.4 1.0
SG B:CYS26 2.4 73.7 1.0
CB B:CYS29 2.8 47.2 1.0
CB B:CYS8 3.0 68.6 1.0
CB B:CYS26 3.1 57.5 1.0
SG B:CYS8 3.2 78.7 1.0
CB B:CYS5 3.3 73.0 1.0
N B:CYS26 3.6 64.4 1.0
N B:CYS8 3.8 71.8 1.0
CA B:CYS26 3.9 66.8 1.0
CA B:CYS8 4.0 72.5 1.0
CA B:CYS29 4.0 48.2 1.0
N B:CYS29 4.1 49.2 1.0
CB B:LEU7 4.3 72.7 1.0
C B:LEU7 4.6 72.3 1.0
CA B:GLY99 4.6 74.5 1.0
C B:CYS26 4.7 71.8 1.0
N B:GLY99 4.7 78.9 1.0
CA B:CYS5 4.7 71.3 1.0
O B:CYS26 4.7 69.3 1.0
C B:LEU25 4.8 62.2 1.0
CB B:SER10 4.8 60.9 1.0
CA B:LEU7 4.8 69.4 1.0
N B:LEU7 4.9 59.5 1.0
OG B:SER100 4.9 68.2 1.0

Zinc binding site 6 out of 6 in 5rlc

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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 Z56923284


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 Z56923284 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:71.2
occ:1.00
 SG B:CYS55 2.2 85.2 1.0
SG B:CYS50 2.4 64.2 1.0
SG B:CYS72 2.7 60.3 1.0
ND1 B:HIS75 2.9 83.2 1.0
CB B:CYS50 3.2 68.3 1.0
CB B:CYS55 3.2 90.7 1.0
CB B:CYS72 3.4 60.9 1.0
CB B:HIS75 3.5 77.3 1.0
CG B:HIS75 3.5 83.2 1.0
N B:CYS72 3.9 55.9 1.0
CE1 B:HIS75 3.9 86.0 1.0
CB B:ALA52 4.1 87.8 1.0
CA B:CYS72 4.2 61.1 1.0
CG2 B:VAL57 4.5 87.8 1.0
N B:HIS75 4.5 68.6 1.0
CA B:HIS75 4.6 76.2 1.0
CA B:CYS55 4.6 95.8 1.0
CA B:CYS50 4.6 72.0 1.0
CD2 B:HIS75 4.7 87.6 1.0
CB B:VAL57 4.8 88.2 1.0
NE2 B:HIS75 4.9 84.9 1.0
C B:CYS72 5.0 64.3 1.0
C B:TYR71 5.0 61.4 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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