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Zinc in PDB 5rlu: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722:
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 Z744754722, PDB code: 5rlu 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) 81.59 / 2.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.209, 70.227, 86.037, 103.13, 96.93, 111.98
R / Rfree (%) 16 / 27.3

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 Z744754722 (pdb code 5rlu). 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 Z744754722, PDB code: 5rlu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlu

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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 Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:89.9
occ:1.00
 ND1 A:HIS75 2.2 80.8 1.0
SG A:CYS55 2.3 94.5 1.0
SG A:CYS50 2.5 92.6 1.0
SG A:CYS72 2.7 91.9 1.0
CG A:HIS75 3.1 77.8 1.0
CE1 A:HIS75 3.2 78.6 1.0
CB A:CYS50 3.3 98.2 1.0
CB A:CYS55 3.3 96.2 1.0
CB A:HIS75 3.4 75.5 1.0
CB A:CYS72 3.4 88.5 1.0
N A:CYS72 3.7 84.1 1.0
CA A:CYS72 4.1 89.6 1.0
N A:HIS75 4.2 77.4 1.0
CD2 A:HIS75 4.3 76.7 1.0
CG2 A:VAL57 4.3 88.7 1.0
NE2 A:HIS75 4.4 76.7 1.0
CA A:HIS75 4.4 77.5 1.0
CB A:ALA52 4.5 80.1 1.0
CB A:VAL57 4.6 87.7 1.0
CA A:CYS55 4.7 0.7 1.0
CA A:CYS50 4.8 97.9 1.0
CB A:SER74 4.8 80.0 1.0
C A:SER74 4.8 80.2 1.0
C A:CYS72 4.8 90.0 1.0
C A:TYR71 4.9 84.2 1.0

Zinc binding site 2 out of 6 in 5rlu

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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 Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:89.5
occ:1.00
 NE2 A:HIS33 1.9 87.5 1.0
SG A:CYS16 2.2 0.2 1.0
ND1 A:HIS39 2.3 96.6 1.0
SG A:CYS19 2.4 90.0 1.0
CE1 A:HIS33 2.8 86.0 1.0
CD2 A:HIS33 3.0 89.5 1.0
CG A:HIS39 3.0 98.9 1.0
CE1 A:HIS39 3.2 0.6 1.0
CB A:HIS39 3.3 99.0 1.0
CB A:CYS16 3.4 0.2 1.0
CB A:CYS19 3.6 87.9 1.0
N A:CYS19 3.6 89.2 1.0
CA A:CYS19 3.9 90.3 1.0
ND1 A:HIS33 4.0 88.1 1.0
CG A:HIS33 4.1 90.5 1.0
CD2 A:HIS39 4.1 98.9 1.0
NE2 A:HIS39 4.2 0.6 1.0
CB A:ALA110 4.3 85.0 1.0
C A:ALA18 4.3 92.8 1.0
CB A:ALA18 4.5 95.6 1.0
CA A:CYS16 4.7 0.8 1.0
CA A:ALA18 4.8 97.5 1.0
CA A:HIS39 4.8 97.7 1.0
N A:ALA18 4.9 96.9 1.0
CE2 A:PHE106 4.9 97.1 1.0
CZ A:PHE106 4.9 0.8 1.0

Zinc binding site 3 out of 6 in 5rlu

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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 Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.3
occ:1.00
 SG A:CYS5 2.2 0.1 1.0
SG A:CYS8 2.7 0.8 1.0
SG A:CYS29 2.7 0.6 1.0
SG A:CYS26 2.9 0.6 1.0
CB A:CYS5 3.1 0.4 1.0
CB A:CYS26 3.2 0.1 1.0
CB A:CYS29 3.3 0.5 1.0
N A:CYS8 3.6 0.8 1.0
N A:CYS26 3.7 0.2 1.0
CB A:CYS8 4.0 0.0 1.0
CA A:CYS26 4.0 0.2 1.0
CA A:CYS8 4.2 0.8 1.0
CB A:LEU7 4.3 0.2 1.0
C A:LEU7 4.3 0.0 1.0
N A:LEU7 4.4 0.1 1.0
CA A:LEU7 4.5 0.2 1.0
CA A:CYS5 4.5 0.1 1.0
CB A:SER10 4.5 0.1 1.0
CA A:CYS29 4.6 0.4 1.0
N A:ASN9 4.6 0.4 1.0
C A:CYS8 4.6 0.4 1.0
N A:SER10 4.6 1.0 1.0
OG A:SER10 4.7 0.5 1.0
N A:CYS29 4.7 0.5 1.0
C A:LEU25 4.8 0.9 1.0
O A:SER10 4.9 0.9 1.0
C A:CYS5 4.9 0.9 1.0
C A:CYS26 5.0 0.7 1.0

Zinc binding site 4 out of 6 in 5rlu

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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 Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:75.8
occ:1.00
 NE2 B:HIS33 1.9 69.9 1.0
ND1 B:HIS39 2.2 80.0 1.0
SG B:CYS16 2.2 72.7 1.0
SG B:CYS19 2.5 79.9 1.0
CE1 B:HIS33 2.9 68.5 1.0
CG B:HIS39 2.9 80.9 1.0
CD2 B:HIS33 3.0 71.5 1.0
CE1 B:HIS39 3.2 80.3 1.0
CB B:HIS39 3.2 81.1 1.0
CB B:CYS16 3.4 76.5 1.0
N B:CYS19 3.6 75.5 1.0
CB B:CYS19 3.6 75.5 1.0
CA B:CYS19 3.9 78.5 1.0
CD2 B:HIS39 4.0 79.9 1.0
ND1 B:HIS33 4.0 68.7 1.0
NE2 B:HIS39 4.1 79.7 1.0
CG B:HIS33 4.1 70.4 1.0
C B:ALA18 4.2 73.0 1.0
CB B:ALA18 4.4 71.5 1.0
CB B:ALA110 4.4 72.7 1.0
CA B:HIS39 4.7 79.8 1.0
CA B:ALA18 4.7 70.0 1.0
CA B:CYS16 4.8 72.0 1.0
N B:ALA18 4.8 74.8 1.0
O B:ALA18 5.0 76.7 1.0

Zinc binding site 5 out of 6 in 5rlu

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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 Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.5
occ:1.00
 SG B:CYS5 2.4 80.5 1.0
SG B:CYS29 2.4 75.8 1.0
SG B:CYS26 2.6 90.7 1.0
SG B:CYS8 2.7 0.7 1.0
CB B:CYS29 3.0 72.3 1.0
CB B:CYS26 3.2 85.0 1.0
CB B:CYS5 3.4 87.5 1.0
N B:CYS26 3.7 84.0 1.0
N B:CYS8 3.8 98.0 1.0
CA B:CYS26 4.0 87.0 1.0
CB B:CYS8 4.1 98.7 1.0
CA B:CYS29 4.3 75.9 1.0
CB B:LEU7 4.3 90.8 1.0
N B:CYS29 4.4 79.1 1.0
CA B:CYS8 4.4 98.0 1.0
C B:LEU7 4.5 97.3 1.0
N B:GLY99 4.6 0.1 1.0
CB B:SER10 4.6 92.7 1.0
N B:LEU7 4.6 87.3 1.0
CA B:LEU7 4.7 88.8 1.0
CA B:GLY99 4.7 99.8 1.0
OG B:SER10 4.7 89.8 1.0
C B:GLY99 4.8 98.9 1.0
O B:GLY99 4.8 95.9 1.0
CA B:CYS5 4.8 87.2 1.0
C B:CYS26 4.9 90.1 1.0
C B:LEU25 4.9 84.6 1.0
C B:CYS8 4.9 97.7 1.0
N B:SER10 4.9 0.6 1.0
N B:ASN9 5.0 0.1 1.0

Zinc binding site 6 out of 6 in 5rlu

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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 Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:1.0
occ:1.00
 SG B:CYS50 2.2 0.8 1.0
ND1 B:HIS75 2.4 0.5 1.0
SG B:CYS55 2.7 0.5 1.0
SG B:CYS72 2.9 0.8 1.0
CG B:HIS75 3.1 0.5 1.0
CB B:HIS75 3.1 0.9 1.0
CB B:CYS50 3.2 0.6 1.0
N B:CYS72 3.5 0.4 1.0
CB B:CYS72 3.5 0.8 1.0
CB B:CYS55 3.5 0.1 1.0
CE1 B:HIS75 3.5 0.1 1.0
N B:HIS75 3.9 0.1 1.0
CA B:CYS72 4.0 0.4 1.0
CB B:ALA52 4.1 0.4 1.0
CA B:HIS75 4.1 0.5 1.0
CD2 B:HIS75 4.3 1.0 1.0
NE2 B:HIS75 4.5 1.0 1.0
C B:SER74 4.6 0.2 1.0
C B:TYR71 4.6 0.3 1.0
C B:CYS72 4.6 0.5 1.0
CA B:CYS50 4.6 0.0 1.0
CA B:TYR71 4.7 0.2 1.0
CG2 B:VAL57 4.8 0.3 1.0
O B:CYS72 4.8 0.9 1.0
CB B:TYR71 4.9 0.7 1.0
CB B:SER74 4.9 0.4 1.0
CA B:CYS55 5.0 0.3 1.0
CB B:VAL57 5.0 0.7 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 04:06:32 2024

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