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Zinc in PDB 5rlw: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45705015

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45705015

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45705015:
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 Z45705015, PDB code: 5rlw 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) 81.20 / 1.97
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.115, 70.113, 85.100, 102.69, 95.96, 112.44
R / Rfree (%) 17.1 / 23.7

Other elements in 5rlw:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45705015 also contains other interesting chemical elements:

Fluorine (F) 2 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 Z45705015 (pdb code 5rlw). 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 Z45705015, PDB code: 5rlw:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlw

Go back to Zinc Binding Sites List in 5rlw
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45705015


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 Z45705015 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:66.1
occ:1.00
 ND1 A:HIS75 2.2 55.7 1.0
SG A:CYS50 2.3 73.1 1.0
SG A:CYS55 2.4 69.6 1.0
SG A:CYS72 2.8 68.9 1.0
CE1 A:HIS75 3.1 55.5 1.0
CB A:CYS50 3.2 72.2 1.0
CG A:HIS75 3.2 55.8 1.0
CB A:CYS55 3.3 72.8 1.0
CB A:CYS72 3.5 72.2 1.0
CB A:HIS75 3.6 55.1 1.0
N A:CYS72 3.8 68.8 1.0
CB A:ALA52 4.1 65.8 1.0
CA A:CYS72 4.2 68.9 1.0
NE2 A:HIS75 4.3 54.2 1.0
CD2 A:HIS75 4.3 54.8 1.0
CG2 A:VAL57 4.5 72.6 1.0
N A:HIS75 4.5 60.6 1.0
CA A:CYS50 4.6 71.0 1.0
CB A:VAL57 4.7 72.0 1.0
CA A:HIS75 4.7 58.1 1.0
CA A:CYS55 4.8 76.0 1.0
C A:TYR71 4.9 64.7 1.0
C A:CYS72 4.9 70.8 1.0

Zinc binding site 2 out of 6 in 5rlw

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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 Z45705015


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 Z45705015 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:66.8
occ:1.00
 NE2 A:HIS33 2.0 55.5 1.0
ND1 A:HIS39 2.1 70.7 1.0
SG A:CYS16 2.3 81.3 1.0
SG A:CYS19 2.4 65.5 1.0
CE1 A:HIS33 2.9 56.2 1.0
CD2 A:HIS33 3.0 57.0 1.0
CE1 A:HIS39 3.0 71.7 1.0
CG A:HIS39 3.0 71.5 1.0
CB A:CYS16 3.3 76.1 1.0
CB A:HIS39 3.4 67.6 1.0
N A:CYS19 3.4 69.5 1.0
CB A:CYS19 3.5 64.5 1.0
CA A:CYS19 3.8 68.0 1.0
ND1 A:HIS33 4.1 58.7 1.0
C A:ALA18 4.1 74.6 1.0
CG A:HIS33 4.1 59.6 1.0
NE2 A:HIS39 4.1 71.4 1.0
CD2 A:HIS39 4.2 71.5 1.0
CB A:ALA110 4.4 57.2 1.0
CB A:ALA18 4.4 73.7 1.0
CA A:ALA18 4.6 73.6 1.0
CA A:CYS16 4.7 75.8 1.0
N A:ALA18 4.7 72.9 1.0
O A:ALA18 4.8 74.8 1.0
CA A:HIS39 4.9 67.0 1.0
CE2 A:PHE106 4.9 60.5 1.0
CZ A:PHE106 5.0 60.9 1.0
C A:CYS16 5.0 74.0 1.0

Zinc binding site 3 out of 6 in 5rlw

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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 Z45705015


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 Z45705015 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:94.3
occ:1.00
 SG A:CYS5 2.2 82.0 1.0
SG A:CYS26 2.4 83.2 1.0
SG A:CYS29 2.6 95.5 1.0
SG A:CYS8 2.6 96.0 1.0
CB A:CYS29 3.1 88.7 1.0
CB A:CYS26 3.3 82.3 1.0
CB A:CYS5 3.3 82.9 1.0
N A:CYS8 3.6 97.5 1.0
CB A:CYS8 3.6 95.7 1.0
N A:CYS26 3.8 78.8 1.0
CA A:CYS26 4.0 83.7 1.0
CA A:CYS8 4.0 99.5 1.0
CB A:LEU7 4.4 87.5 1.0
CA A:CYS29 4.4 83.3 1.0
N A:CYS29 4.4 87.2 1.0
C A:CYS8 4.6 0.2 1.0
C A:LEU7 4.6 94.6 1.0
O A:CYS26 4.6 80.9 1.0
C A:CYS26 4.7 84.6 1.0
CA A:CYS5 4.7 82.2 1.0
CB A:SER10 4.7 96.0 1.0
CA A:LEU7 4.8 87.8 1.0
N A:LEU7 4.9 84.5 1.0
N A:ASN9 4.9 0.0 1.0
OG A:SER10 4.9 89.0 1.0
C A:LEU25 5.0 77.0 1.0

Zinc binding site 4 out of 6 in 5rlw

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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 Z45705015


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 Z45705015 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:35.9
occ:1.00
 NE2 B:HIS33 2.0 50.6 1.0
ND1 B:HIS39 2.2 38.7 1.0
SG B:CYS16 2.2 41.4 1.0
SG B:CYS19 2.6 46.6 1.0
CD2 B:HIS33 3.0 49.3 1.0
CG B:HIS39 3.0 44.0 1.0
CE1 B:HIS33 3.1 48.5 1.0
CE1 B:HIS39 3.1 42.4 1.0
CB B:HIS39 3.3 44.8 1.0
CB B:CYS19 3.4 48.5 1.0
N B:CYS19 3.5 48.9 1.0
CB B:CYS16 3.5 46.1 1.0
CA B:CYS19 3.8 49.2 1.0
C B:ALA18 4.1 48.4 1.0
CG B:HIS33 4.1 49.4 1.0
CD2 B:HIS39 4.2 45.5 1.0
ND1 B:HIS33 4.2 47.4 1.0
NE2 B:HIS39 4.2 45.2 1.0
CB B:ALA18 4.4 46.2 1.0
N B:ALA18 4.6 49.2 1.0
CB B:ALA110 4.6 41.7 1.0
CA B:ALA18 4.6 46.8 1.0
CA B:HIS39 4.7 46.9 1.0
CA B:CYS16 4.8 43.9 1.0
O B:ALA18 4.9 48.7 1.0
C B:CYS16 4.9 45.6 1.0

Zinc binding site 5 out of 6 in 5rlw

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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 Z45705015


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 Z45705015 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:63.3
occ:1.00
 SG B:CYS26 2.3 60.2 1.0
SG B:CYS5 2.3 64.6 1.0
SG B:CYS29 2.3 58.2 1.0
CB B:CYS8 2.5 76.6 1.0
CB B:CYS29 3.0 54.2 1.0
SG B:CYS8 3.3 87.8 1.0
CB B:CYS5 3.4 69.2 1.0
CB B:CYS26 3.5 59.9 1.0
CA B:CYS8 3.8 75.6 1.0
N B:CYS8 3.8 74.9 1.0
N B:CYS26 3.9 59.3 1.0
N B:CYS29 4.0 53.9 1.0
CA B:CYS29 4.1 53.3 1.0
CA B:CYS26 4.2 57.9 1.0
CB B:LEU7 4.6 73.6 1.0
CB B:SER10 4.6 74.4 1.0
C B:LEU7 4.7 72.2 1.0
OG B:SER10 4.7 69.5 1.0
N B:GLY99 4.7 82.2 1.0
CA B:GLY99 4.8 79.7 1.0
C B:CYS8 4.8 75.8 1.0
CA B:CYS5 4.8 68.1 1.0
C B:CYS26 4.9 59.8 1.0
N B:ASN9 5.0 78.1 1.0
C B:LEU25 5.0 57.0 1.0
N B:LEU7 5.0 67.0 1.0

Zinc binding site 6 out of 6 in 5rlw

Go back to Zinc Binding Sites List in 5rlw
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45705015


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 Z45705015 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:79.9
occ:1.00
 SG B:CYS50 2.2 73.9 1.0
ND1 B:HIS75 2.2 80.7 1.0
SG B:CYS55 2.4 0.8 1.0
SG B:CYS72 2.9 81.7 1.0
CB B:CYS50 3.1 77.4 1.0
CE1 B:HIS75 3.2 80.2 1.0
CG B:HIS75 3.2 79.0 1.0
CB B:CYS55 3.3 0.7 1.0
CB B:CYS72 3.5 77.8 1.0
CB B:HIS75 3.5 76.9 1.0
N B:CYS72 3.7 75.5 1.0
CB B:ALA52 4.1 94.1 1.0
CA B:CYS72 4.2 77.7 1.0
NE2 B:HIS75 4.3 82.3 1.0
CD2 B:HIS75 4.4 80.9 1.0
N B:HIS75 4.5 76.0 1.0
CG2 B:VAL57 4.5 80.3 1.0
CA B:CYS50 4.5 76.9 1.0
CA B:HIS75 4.6 77.8 1.0
CB B:VAL57 4.7 82.2 1.0
CA B:CYS55 4.8 0.4 1.0
C B:TYR71 4.8 73.4 1.0
C B:CYS72 4.9 77.1 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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