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Zinc in PDB 5rly: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2027049478

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2027049478

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2027049478:
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 Z2027049478, PDB code: 5rly 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) 62.26 / 2.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.151, 70.144, 85.263, 102.15, 96.51, 112.54
R / Rfree (%) 15.4 / 26.1

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 Z2027049478 (pdb code 5rly). 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 Z2027049478, PDB code: 5rly:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rly

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:78.3
occ:1.00
 SG A:CYS55 2.4 79.3 1.0
SG A:CYS50 2.4 74.4 1.0
ND1 A:HIS75 2.5 73.4 1.0
SG A:CYS72 2.7 94.1 1.0
CB A:CYS72 3.3 87.7 1.0
CE1 A:HIS75 3.3 72.4 1.0
CB A:CYS55 3.4 81.8 1.0
CB A:CYS50 3.4 83.4 1.0
CG A:HIS75 3.4 70.5 1.0
N A:CYS72 3.7 80.7 1.0
CB A:HIS75 3.7 68.0 1.0
CA A:CYS72 4.1 84.4 1.0
N A:HIS75 4.2 68.9 1.0
CB A:ALA52 4.3 79.8 1.0
CG2 A:VAL57 4.4 84.5 1.0
NE2 A:HIS75 4.4 67.8 1.0
CD2 A:HIS75 4.5 68.7 1.0
CB A:VAL57 4.6 86.3 1.0
CA A:HIS75 4.6 68.3 1.0
C A:CYS72 4.8 86.3 1.0
CA A:CYS55 4.8 85.9 1.0
CB A:SER74 4.8 74.2 1.0
CA A:CYS50 4.8 83.6 1.0
C A:TYR71 4.9 75.8 1.0
C A:SER74 5.0 74.3 1.0

Zinc binding site 2 out of 6 in 5rly

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:78.7
occ:1.00
 NE2 A:HIS33 2.0 69.2 1.0
ND1 A:HIS39 2.3 99.2 1.0
SG A:CYS16 2.3 89.8 1.0
SG A:CYS19 2.4 83.2 1.0
CE1 A:HIS33 2.8 69.5 1.0
CG A:HIS39 3.1 98.8 1.0
CE1 A:HIS39 3.2 98.8 1.0
CD2 A:HIS33 3.3 69.8 1.0
CB A:HIS39 3.4 95.7 1.0
CB A:CYS16 3.4 92.4 1.0
CB A:CYS19 3.5 81.5 1.0
N A:CYS19 3.6 88.7 1.0
CA A:CYS19 3.8 88.2 1.0
ND1 A:HIS33 4.0 69.9 1.0
CD2 A:HIS39 4.1 0.6 1.0
NE2 A:HIS39 4.1 0.1 1.0
C A:ALA18 4.1 92.7 1.0
CG A:HIS33 4.2 73.8 1.0
CB A:ALA110 4.3 80.0 1.0
CB A:ALA18 4.6 92.6 1.0
CA A:ALA18 4.7 92.7 1.0
O A:ALA18 4.7 90.3 1.0
CA A:CYS16 4.7 93.8 1.0
N A:ALA18 4.8 92.8 1.0
CA A:HIS39 4.9 90.7 1.0
O A:CYS16 5.0 89.8 1.0
CE2 A:PHE106 5.0 88.3 1.0

Zinc binding site 3 out of 6 in 5rly

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.3
occ:1.00
 SG A:CYS26 2.3 0.6 1.0
SG A:CYS5 2.3 0.3 1.0
SG A:CYS8 2.5 0.2 1.0
SG A:CYS29 2.6 0.2 1.0
CB A:CYS29 3.2 0.3 1.0
CB A:CYS8 3.3 0.7 1.0
CB A:CYS26 3.4 0.9 1.0
CB A:CYS5 3.4 0.9 1.0
N A:CYS8 3.5 0.3 1.0
CA A:CYS8 3.9 0.1 1.0
N A:CYS26 4.0 0.2 1.0
CB A:LEU7 4.2 0.1 1.0
CA A:CYS26 4.3 0.3 1.0
N A:CYS29 4.3 0.9 1.0
C A:LEU7 4.3 0.9 1.0
CA A:CYS29 4.4 99.6 1.0
C A:CYS8 4.5 0.5 1.0
CA A:LEU7 4.7 0.4 1.0
N A:ASN9 4.8 0.6 1.0
CB A:SER10 4.8 0.9 1.0
CA A:CYS5 4.8 0.5 1.0
N A:LEU7 4.8 0.2 1.0
OG A:SER10 4.9 0.5 1.0
O A:CYS26 4.9 0.2 1.0
C A:CYS26 4.9 0.7 1.0

Zinc binding site 4 out of 6 in 5rly

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:64.5
occ:1.00
 NE2 B:HIS33 2.0 69.0 1.0
SG B:CYS16 2.1 69.4 1.0
ND1 B:HIS39 2.3 71.0 1.0
SG B:CYS19 2.5 65.7 1.0
CE1 B:HIS33 2.9 70.6 1.0
CG B:HIS39 3.0 69.0 1.0
CD2 B:HIS33 3.2 70.3 1.0
CE1 B:HIS39 3.2 71.4 1.0
CB B:CYS16 3.3 69.7 1.0
CB B:HIS39 3.3 67.4 1.0
N B:CYS19 3.5 71.6 1.0
CB B:CYS19 3.6 69.8 1.0
CA B:CYS19 3.8 71.5 1.0
ND1 B:HIS33 4.1 70.8 1.0
C B:ALA18 4.1 67.5 1.0
CD2 B:HIS39 4.1 69.8 1.0
NE2 B:HIS39 4.2 72.6 1.0
CG B:HIS33 4.2 70.2 1.0
CB B:ALA110 4.5 53.6 1.0
CB B:ALA18 4.5 58.6 1.0
CA B:CYS16 4.6 70.0 1.0
CA B:ALA18 4.6 65.0 1.0
N B:ALA18 4.7 66.3 1.0
O B:ALA18 4.7 67.1 1.0
CA B:HIS39 4.8 67.8 1.0
O B:CYS16 4.8 69.6 1.0
C B:CYS16 4.9 70.1 1.0

Zinc binding site 5 out of 6 in 5rly

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:93.7
occ:1.00
 SG B:CYS26 2.3 75.3 1.0
SG B:CYS5 2.3 84.7 1.0
SG B:CYS29 2.5 77.4 1.0
CB B:CYS8 2.7 94.6 1.0
CB B:CYS29 3.0 69.6 1.0
SG B:CYS8 3.2 98.0 1.0
CB B:CYS26 3.4 78.1 1.0
CB B:CYS5 3.5 92.3 1.0
N B:CYS8 3.6 91.0 1.0
CA B:CYS8 3.8 92.2 1.0
N B:CYS26 3.9 81.7 1.0
N B:CYS29 4.2 74.3 1.0
CA B:CYS29 4.2 70.3 1.0
CA B:CYS26 4.2 78.2 1.0
CB B:LEU7 4.3 92.2 1.0
C B:LEU7 4.4 89.8 1.0
N B:GLY99 4.7 88.2 1.0
CA B:GLY99 4.8 88.6 1.0
CA B:LEU7 4.8 89.3 1.0
C B:CYS8 4.8 92.0 1.0
O B:CYS26 4.8 82.3 1.0
CA B:CYS5 4.9 89.9 1.0
CB B:SER10 4.9 80.5 1.0
C B:CYS26 4.9 80.7 1.0
N B:LEU7 4.9 90.9 1.0
N B:ASN9 4.9 92.5 1.0
OG B:SER10 4.9 73.4 1.0

Zinc binding site 6 out of 6 in 5rly

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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 Z2027049478


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 Z2027049478 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:0.3
occ:1.00
 SG B:CYS50 2.2 91.2 1.0
SG B:CYS55 2.3 0.1 1.0
ND1 B:HIS75 2.6 95.0 1.0
SG B:CYS72 2.9 99.5 1.0
CB B:CYS50 3.2 99.6 1.0
CB B:CYS55 3.2 0.5 1.0
CE1 B:HIS75 3.4 93.8 1.0
CB B:CYS72 3.5 97.3 1.0
CG B:HIS75 3.5 96.1 1.0
N B:CYS72 3.7 94.2 1.0
CB B:HIS75 3.7 96.3 1.0
CB B:ALA52 4.1 0.7 1.0
CA B:CYS72 4.1 95.3 1.0
N B:HIS75 4.4 92.8 1.0
CG2 B:VAL57 4.5 96.1 1.0
NE2 B:HIS75 4.5 95.3 1.0
CD2 B:HIS75 4.5 95.2 1.0
CA B:CYS50 4.6 0.2 1.0
CB B:VAL57 4.6 96.2 1.0
CA B:CYS55 4.7 0.1 1.0
CA B:HIS75 4.7 96.4 1.0
C B:TYR71 4.8 92.5 1.0
C B:CYS72 4.9 96.9 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 04:11:58 2024

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