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Zinc in PDB 5rm3: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474:
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 Z1745658474, PDB code: 5rm3 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) 81.27 / 2.09
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.130, 70.161, 85.280, 102.81, 96.13, 112.39
R / Rfree (%) 21.6 / 27.4

Other elements in 5rm3:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474 also contains other interesting chemical elements:

Fluorine (F) 3 atoms

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 Z1745658474 (pdb code 5rm3). 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 Z1745658474, PDB code: 5rm3:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm3

Go back to Zinc Binding Sites List in 5rm3
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:42.0
occ:1.00
 SG B:CYS16 2.1 42.7 1.0
NE2 B:HIS33 2.1 33.2 1.0
ND1 B:HIS39 2.1 52.9 1.0
SG B:CYS19 2.5 44.6 1.0
CG B:HIS39 3.0 57.6 1.0
CD2 B:HIS33 3.0 34.8 1.0
CE1 B:HIS39 3.1 57.2 1.0
CB B:CYS16 3.2 45.9 1.0
CE1 B:HIS33 3.2 38.5 1.0
CB B:HIS39 3.3 52.6 1.0
CB B:CYS19 3.4 44.5 1.0
N B:CYS19 3.4 54.5 1.0
CA B:CYS19 3.8 50.0 1.0
CD2 B:HIS39 4.1 54.1 1.0
NE2 B:HIS39 4.1 54.7 1.0
CG B:HIS33 4.2 38.9 1.0
ND1 B:HIS33 4.3 33.7 1.0
C B:ALA18 4.3 54.9 1.0
CB B:ALA18 4.5 50.1 1.0
CB B:ALA110 4.5 41.2 1.0
CA B:CYS16 4.6 50.6 1.0
CA B:HIS39 4.7 49.4 1.0
CA B:ALA18 4.8 50.9 1.0
N B:ALA18 4.8 53.3 1.0
C B:CYS16 4.9 51.3 1.0

Zinc binding site 2 out of 6 in 5rm3

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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 Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:69.4
occ:1.00
 SG B:CYS5 2.0 75.3 1.0
SG B:CYS26 2.2 92.7 1.0
SG B:CYS29 2.4 68.2 1.0
CB B:CYS29 2.9 62.9 1.0
CB B:CYS26 3.0 64.7 1.0
CB B:CYS5 3.2 83.5 1.0
CB B:CYS8 3.2 93.9 1.0
SG B:CYS8 3.3 84.7 1.0
N B:CYS26 3.7 76.7 1.0
CA B:CYS26 3.8 75.5 1.0
N B:CYS8 3.8 89.5 1.0
N B:CYS29 4.1 58.9 1.0
CA B:CYS29 4.1 56.8 1.0
CA B:CYS8 4.1 91.4 1.0
O B:CYS26 4.2 66.8 1.0
CB B:SER10 4.4 70.0 1.0
C B:CYS26 4.4 75.8 1.0
CB B:LEU7 4.5 88.6 1.0
CA B:CYS5 4.5 82.8 1.0
N B:GLY99 4.6 72.7 1.0
O B:CYS5 4.7 73.8 1.0
CA B:GLY99 4.7 69.0 1.0
C B:LEU7 4.7 82.0 1.0
OG B:SER10 4.8 68.0 1.0
C B:CYS5 4.9 77.1 1.0
C B:LEU25 4.9 70.7 1.0
N B:LEU7 5.0 74.1 1.0
N B:ASN9 5.0 76.5 1.0
CA B:LEU7 5.0 86.2 1.0

Zinc binding site 3 out of 6 in 5rm3

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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 Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:76.1
occ:1.00
 SG B:CYS55 2.3 74.6 1.0
SG B:CYS50 2.4 70.2 1.0
ND1 B:HIS75 2.4 76.3 1.0
SG B:CYS72 2.6 62.2 1.0
CB B:CYS55 3.1 81.9 1.0
CE1 B:HIS75 3.3 78.7 1.0
CG B:HIS75 3.3 79.4 1.0
CB B:CYS50 3.5 78.6 1.0
CB B:CYS72 3.5 64.5 1.0
CB B:HIS75 3.6 75.7 1.0
CB B:ALA52 3.8 94.5 1.0
N B:CYS72 3.9 60.0 1.0
CA B:CYS72 4.3 66.8 1.0
N B:HIS75 4.3 65.4 1.0
CG2 B:VAL57 4.4 71.8 1.0
NE2 B:HIS75 4.4 78.5 1.0
CD2 B:HIS75 4.4 80.4 1.0
CA B:CYS55 4.6 86.3 1.0
CA B:HIS75 4.6 72.1 1.0
CB B:VAL57 4.7 78.0 1.0
CA B:CYS50 4.9 80.2 1.0
CB B:SER74 4.9 65.0 1.0
C B:TYR71 5.0 66.8 1.0
C B:CYS72 5.0 71.2 1.0

Zinc binding site 4 out of 6 in 5rm3

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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 Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:53.2
occ:1.00
 SG A:CYS55 2.1 57.4 1.0
SG A:CYS50 2.2 51.4 1.0
ND1 A:HIS75 2.2 41.4 1.0
SG A:CYS72 2.5 47.8 1.0
CB A:CYS55 3.1 56.7 1.0
CE1 A:HIS75 3.1 40.8 1.0
CB A:CYS50 3.2 53.7 1.0
CG A:HIS75 3.3 37.6 1.0
CB A:CYS72 3.5 55.8 1.0
CB A:HIS75 3.6 41.2 1.0
N A:CYS72 3.9 52.3 1.0
CB A:ALA52 4.1 52.1 1.0
CA A:CYS72 4.2 52.9 1.0
NE2 A:HIS75 4.3 39.1 1.0
CD2 A:HIS75 4.3 40.0 1.0
CA A:CYS55 4.5 59.4 1.0
CA A:CYS50 4.6 54.6 1.0
CG2 A:VAL57 4.7 52.1 1.0
N A:HIS75 4.7 49.5 1.0
CB A:VAL57 4.8 52.9 1.0
CA A:HIS75 4.8 44.6 1.0
CB A:SER74 5.0 62.9 1.0
C A:CYS72 5.0 58.4 1.0
C A:TYR71 5.0 48.7 1.0

Zinc binding site 5 out of 6 in 5rm3

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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 Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:54.6
occ:1.00
 NE2 A:HIS33 1.8 29.7 1.0
ND1 A:HIS39 2.0 50.8 1.0
SG A:CYS16 2.4 66.3 1.0
SG A:CYS19 2.4 58.0 1.0
CE1 A:HIS33 2.7 37.1 1.0
CE1 A:HIS39 2.9 59.7 1.0
CD2 A:HIS33 2.9 38.6 1.0
N A:CYS19 3.0 52.5 1.0
CG A:HIS39 3.1 62.7 1.0
CB A:CYS16 3.3 66.1 1.0
CB A:CYS19 3.5 47.0 1.0
CB A:HIS39 3.5 60.9 1.0
CA A:CYS19 3.7 54.5 1.0
ND1 A:HIS33 3.9 38.3 1.0
CB A:ALA18 4.0 66.3 1.0
CG A:HIS33 4.0 39.8 1.0
C A:ALA18 4.0 63.3 1.0
NE2 A:HIS39 4.0 57.8 1.0
CD2 A:HIS39 4.1 66.8 1.0
CA A:ALA18 4.3 66.0 1.0
N A:ALA18 4.5 60.8 1.0
CB A:ALA110 4.5 58.1 1.0
CA A:CYS16 4.7 62.9 1.0
CA A:HIS39 4.9 58.6 1.0
C A:CYS16 4.9 54.9 1.0
CE2 A:PHE106 4.9 53.4 1.0
O A:ALA18 5.0 65.0 1.0

Zinc binding site 6 out of 6 in 5rm3

Go back to Zinc Binding Sites List in 5rm3
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1745658474


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 Z1745658474 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:81.7
occ:1.00
 SG A:CYS5 2.3 82.8 1.0
SG A:CYS29 2.5 77.1 1.0
SG A:CYS8 2.6 0.2 1.0
SG A:CYS26 2.7 67.5 1.0
CB A:CYS26 3.0 68.8 1.0
CB A:CYS29 3.0 81.7 1.0
CB A:CYS8 3.5 1.0 1.0
CB A:CYS5 3.5 86.2 1.0
N A:CYS26 3.7 68.6 1.0
N A:CYS8 3.8 0.2 1.0
CA A:CYS26 3.9 72.4 1.0
CA A:CYS8 4.2 0.0 1.0
CA A:CYS29 4.3 76.7 1.0
O A:CYS26 4.3 92.0 1.0
N A:CYS29 4.3 77.0 1.0
CB A:LEU7 4.4 88.0 1.0
C A:CYS26 4.5 82.5 1.0
C A:LEU7 4.6 94.6 1.0
O A:CYS5 4.8 79.6 1.0
CA A:CYS5 4.9 87.8 1.0
CA A:LEU7 4.9 88.7 1.0
C A:CYS8 4.9 0.9 1.0
N A:LEU7 4.9 81.6 1.0
C A:LEU25 5.0 72.7 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 04:11:57 2024

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