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Zinc in PDB 5rlh: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434778

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434778

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434778:
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 Z2856434778, PDB code: 5rlh 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) 81.46 / 2.38
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.048, 70.135, 85.611, 103.03, 96.20, 112.29
R / Rfree (%) 15.6 / 25.1

Other elements in 5rlh:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434778 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 Z2856434778 (pdb code 5rlh). 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 Z2856434778, PDB code: 5rlh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlh

Go back to Zinc Binding Sites List in 5rlh
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:77.2
occ:1.00
 SG A:CYS55 2.3 79.5 1.0
ND1 A:HIS75 2.3 70.3 1.0
SG A:CYS50 2.4 67.0 1.0
SG A:CYS72 3.0 88.8 1.0
CB A:CYS72 3.3 85.5 1.0
CG A:HIS75 3.3 68.9 1.0
CB A:CYS55 3.3 81.5 1.0
CB A:CYS50 3.3 76.6 1.0
CE1 A:HIS75 3.3 68.4 1.0
CB A:HIS75 3.5 68.4 1.0
N A:CYS72 3.8 76.1 1.0
CA A:CYS72 4.1 80.7 1.0
CB A:ALA52 4.2 72.0 1.0
CG2 A:VAL57 4.3 78.0 1.0
N A:HIS75 4.4 73.5 1.0
CD2 A:HIS75 4.5 66.8 1.0
NE2 A:HIS75 4.5 66.0 1.0
CB A:VAL57 4.6 78.5 1.0
CA A:HIS75 4.6 70.4 1.0
CA A:CYS55 4.8 84.7 1.0
CA A:CYS50 4.8 79.3 1.0
C A:CYS72 4.8 82.1 1.0
C A:TYR71 4.9 72.4 1.0

Zinc binding site 2 out of 6 in 5rlh

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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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.8
occ:1.00
 NE2 A:HIS33 2.0 69.9 1.0
ND1 A:HIS39 2.0 92.5 1.0
SG A:CYS16 2.3 98.7 1.0
SG A:CYS19 2.4 87.5 1.0
CE1 A:HIS33 2.9 71.8 1.0
CG A:HIS39 3.0 91.3 1.0
CE1 A:HIS39 3.0 93.7 1.0
CD2 A:HIS33 3.1 72.6 1.0
CB A:HIS39 3.3 87.9 1.0
CB A:CYS16 3.4 96.8 1.0
CB A:CYS19 3.5 84.4 1.0
N A:CYS19 3.6 85.8 1.0
CA A:CYS19 3.8 88.7 1.0
ND1 A:HIS33 4.1 72.8 1.0
CG A:HIS33 4.2 74.9 1.0
NE2 A:HIS39 4.2 91.9 1.0
CD2 A:HIS39 4.2 93.0 1.0
C A:ALA18 4.2 90.2 1.0
CB A:ALA110 4.4 66.0 1.0
CB A:ALA18 4.6 88.3 1.0
CA A:ALA18 4.7 90.7 1.0
CA A:CYS16 4.8 96.7 1.0
O A:ALA18 4.8 89.2 1.0
CA A:HIS39 4.8 86.2 1.0
N A:ALA18 4.9 90.4 1.0

Zinc binding site 3 out of 6 in 5rlh

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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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.9
occ:1.00
 SG A:CYS29 2.2 0.8 1.0
SG A:CYS26 2.3 0.7 1.0
SG A:CYS8 2.6 0.1 1.0
SG A:CYS5 2.6 1.0 1.0
CB A:CYS8 3.2 0.3 1.0
CB A:CYS29 3.2 0.1 1.0
N A:CYS8 3.4 0.1 1.0
CB A:CYS26 3.6 0.4 1.0
CB A:CYS5 3.7 0.5 1.0
CA A:CYS8 3.7 0.0 1.0
CB A:LEU7 4.2 0.4 1.0
N A:CYS29 4.3 0.9 1.0
N A:CYS26 4.3 0.0 1.0
C A:LEU7 4.3 0.0 1.0
CA A:CYS29 4.4 0.1 1.0
C A:CYS8 4.4 0.2 1.0
CA A:CYS26 4.5 0.4 1.0
N A:ASN9 4.7 0.5 1.0
CA A:LEU7 4.7 0.1 1.0
OG A:SER10 4.7 0.1 1.0
N A:LEU7 4.9 0.9 1.0
CB A:SER10 5.0 0.7 1.0
O A:CYS26 5.0 0.8 1.0

Zinc binding site 4 out of 6 in 5rlh

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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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:57.7
occ:1.00
 NE2 B:HIS33 2.0 56.3 1.0
ND1 B:HIS39 2.1 62.7 1.0
SG B:CYS16 2.2 54.1 1.0
SG B:CYS19 2.5 58.2 1.0
CD2 B:HIS33 3.0 57.6 1.0
CE1 B:HIS33 3.0 56.6 1.0
CG B:HIS39 3.1 65.3 1.0
CE1 B:HIS39 3.2 62.6 1.0
CB B:CYS16 3.3 57.4 1.0
CB B:HIS39 3.3 65.6 1.0
CB B:CYS19 3.4 60.8 1.0
N B:CYS19 3.6 62.3 1.0
CA B:CYS19 3.8 63.0 1.0
CG B:HIS33 4.1 57.3 1.0
ND1 B:HIS33 4.1 56.9 1.0
C B:ALA18 4.2 61.7 1.0
CD2 B:HIS39 4.2 65.2 1.0
NE2 B:HIS39 4.3 63.7 1.0
CB B:ALA110 4.5 58.0 1.0
CB B:ALA18 4.6 56.8 1.0
CA B:CYS16 4.6 60.1 1.0
CA B:ALA18 4.7 60.9 1.0
CA B:HIS39 4.8 66.8 1.0
N B:ALA18 4.8 63.1 1.0
O B:ALA18 4.9 62.8 1.0
C B:CYS16 5.0 61.4 1.0

Zinc binding site 5 out of 6 in 5rlh

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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 Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:81.8
occ:1.00
 SG B:CYS5 2.2 79.8 1.0
SG B:CYS26 2.3 75.6 1.0
SG B:CYS29 2.6 63.0 1.0
CB B:CYS8 2.7 0.2 1.0
CB B:CYS29 3.2 65.4 1.0
CB B:CYS5 3.2 83.0 1.0
SG B:CYS8 3.4 0.9 1.0
CB B:CYS26 3.4 74.0 1.0
N B:CYS8 3.6 95.8 1.0
CA B:CYS8 3.7 98.5 1.0
N B:CYS26 4.0 71.9 1.0
CA B:CYS26 4.3 72.5 1.0
N B:CYS29 4.3 68.6 1.0
CA B:CYS29 4.4 66.5 1.0
OG B:SER10 4.5 90.0 1.0
CB B:LEU7 4.5 89.0 1.0
C B:LEU7 4.5 91.6 1.0
N B:ASN9 4.6 97.7 1.0
CA B:CYS5 4.6 82.6 1.0
C B:CYS8 4.6 0.2 1.0
CB B:SER10 4.7 91.0 1.0
N B:GLY99 4.7 99.8 1.0
N B:SER10 4.8 93.0 1.0
CA B:GLY99 4.9 99.8 1.0
C B:CYS26 4.9 73.6 1.0
N B:LEU7 4.9 86.6 1.0
O B:CYS26 4.9 76.5 1.0
CA B:LEU7 4.9 88.6 1.0

Zinc binding site 6 out of 6 in 5rlh

Go back to Zinc Binding Sites List in 5rlh
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434778


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 Z2856434778 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:0.6
occ:1.00
 SG B:CYS50 2.3 99.2 1.0
ND1 B:HIS75 2.4 0.3 1.0
SG B:CYS55 2.4 0.8 1.0
SG B:CYS72 3.0 0.5 1.0
CB B:CYS50 3.3 99.2 1.0
CG B:HIS75 3.3 0.9 1.0
CB B:CYS72 3.3 97.4 1.0
CB B:CYS55 3.4 0.1 1.0
CE1 B:HIS75 3.4 0.9 1.0
CB B:HIS75 3.4 0.3 1.0
N B:CYS72 3.7 91.1 1.0
CA B:CYS72 4.0 96.2 1.0
CB B:ALA52 4.2 0.4 1.0
CG2 B:VAL57 4.3 0.0 1.0
N B:HIS75 4.4 0.2 1.0
CD2 B:HIS75 4.5 0.7 1.0
NE2 B:HIS75 4.5 0.2 1.0
CA B:HIS75 4.6 0.2 1.0
CB B:VAL57 4.6 0.5 1.0
CA B:CYS50 4.7 0.5 1.0
CA B:CYS55 4.8 0.0 1.0
C B:CYS72 4.8 97.3 1.0
C B:TYR71 4.9 87.7 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 04:00:43 2024

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