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Zinc in PDB 5rmh: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1101755952

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1101755952

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1101755952:
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 Z1101755952, PDB code: 5rmh 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) 81.31 / 2.02
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.028, 70.153, 85.181, 102.78, 95.72, 112.55
R / Rfree (%) 16.3 / 24.3

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 Z1101755952 (pdb code 5rmh). 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 Z1101755952, PDB code: 5rmh:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmh

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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 Z1101755952


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 Z1101755952 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.7
occ:1.00
 SG A:CYS50 2.3 65.3 1.0
ND1 A:HIS75 2.3 69.2 1.0
SG A:CYS55 2.4 78.6 1.0
SG A:CYS72 2.9 81.1 1.0
CB A:CYS50 3.3 71.3 1.0
CE1 A:HIS75 3.3 68.5 1.0
CB A:CYS72 3.4 79.0 1.0
CG A:HIS75 3.4 68.8 1.0
CB A:CYS55 3.4 79.0 1.0
CB A:HIS75 3.7 66.2 1.0
N A:CYS72 3.8 73.0 1.0
CA A:CYS72 4.1 75.2 1.0
CG2 A:VAL57 4.3 72.5 1.0
CB A:ALA52 4.4 71.5 1.0
NE2 A:HIS75 4.4 68.9 1.0
CD2 A:HIS75 4.5 69.1 1.0
N A:HIS75 4.5 71.2 1.0
CB A:VAL57 4.6 73.5 1.0
CA A:CYS50 4.7 72.3 1.0
CA A:HIS75 4.8 68.4 1.0
CA A:CYS55 4.8 81.4 1.0
C A:CYS72 4.9 79.0 1.0
C A:TYR71 4.9 66.2 1.0

Zinc binding site 2 out of 6 in 5rmh

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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 Z1101755952


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 Z1101755952 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:67.5
occ:1.00
 NE2 A:HIS33 2.0 64.0 1.0
ND1 A:HIS39 2.3 82.5 1.0
SG A:CYS16 2.3 85.5 1.0
SG A:CYS19 2.4 71.3 1.0
CE1 A:HIS33 2.9 64.2 1.0
CG A:HIS39 3.0 81.5 1.0
CE1 A:HIS39 3.1 84.9 1.0
CD2 A:HIS33 3.2 66.8 1.0
CB A:HIS39 3.4 78.8 1.0
N A:CYS19 3.5 73.2 1.0
CB A:CYS19 3.5 69.7 1.0
CB A:CYS16 3.5 84.6 1.0
CA A:CYS19 3.8 72.8 1.0
CD2 A:HIS39 4.0 83.6 1.0
C A:ALA18 4.0 77.6 1.0
NE2 A:HIS39 4.0 86.0 1.0
ND1 A:HIS33 4.1 66.6 1.0
CG A:HIS33 4.2 69.3 1.0
CB A:ALA110 4.3 64.5 1.0
CB A:ALA18 4.5 78.7 1.0
CA A:ALA18 4.6 78.2 1.0
O A:ALA18 4.6 78.7 1.0
N A:ALA18 4.7 77.2 1.0
CA A:HIS39 4.9 76.8 1.0
CA A:CYS16 4.9 83.2 1.0
CE2 A:PHE106 4.9 72.3 1.0

Zinc binding site 3 out of 6 in 5rmh

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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 Z1101755952


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 Z1101755952 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.3
occ:1.00
 SG A:CYS5 2.3 96.3 1.0
SG A:CYS8 2.4 97.5 1.0
SG A:CYS26 2.4 92.3 1.0
SG A:CYS29 2.5 94.0 1.0
CB A:CYS29 3.2 91.2 1.0
CB A:CYS26 3.4 91.5 1.0
CB A:CYS8 3.4 95.4 1.0
CB A:CYS5 3.5 94.5 1.0
N A:CYS8 3.6 0.7 1.0
N A:CYS26 3.8 88.0 1.0
CA A:CYS8 4.0 0.2 1.0
CA A:CYS26 4.2 93.2 1.0
CB A:LEU7 4.2 99.5 1.0
C A:LEU7 4.3 0.2 1.0
N A:CYS29 4.4 87.2 1.0
CA A:CYS29 4.4 85.4 1.0
CA A:LEU7 4.6 97.1 1.0
OG A:SER10 4.6 97.7 1.0
C A:CYS8 4.7 0.9 1.0
CB A:SER10 4.7 0.9 1.0
N A:LEU7 4.7 97.3 1.0
N A:ASN9 4.8 0.7 1.0
CA A:CYS5 4.8 94.5 1.0
O A:CYS26 4.9 92.6 1.0
C A:CYS26 4.9 93.8 1.0

Zinc binding site 4 out of 6 in 5rmh

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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 Z1101755952


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 Z1101755952 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:39.9
occ:1.00
 NE2 B:HIS33 2.0 64.2 1.0
SG B:CYS16 2.3 40.3 1.0
ND1 B:HIS39 2.3 52.2 1.0
SG B:CYS19 2.5 60.5 1.0
CE1 B:HIS33 2.9 64.9 1.0
CG B:HIS39 3.0 57.9 1.0
CD2 B:HIS33 3.1 63.9 1.0
CE1 B:HIS39 3.1 55.7 1.0
CB B:HIS39 3.2 58.8 1.0
N B:CYS19 3.5 65.7 1.0
CB B:CYS16 3.5 50.1 1.0
CB B:CYS19 3.6 60.9 1.0
CA B:CYS19 3.9 63.1 1.0
CD2 B:HIS39 4.0 59.4 1.0
C B:ALA18 4.0 63.1 1.0
NE2 B:HIS39 4.1 57.3 1.0
ND1 B:HIS33 4.1 63.4 1.0
CG B:HIS33 4.2 65.3 1.0
CB B:ALA18 4.4 56.7 1.0
CB B:ALA110 4.5 48.3 1.0
CA B:ALA18 4.6 60.9 1.0
N B:ALA18 4.6 64.1 1.0
O B:ALA18 4.7 67.4 1.0
CA B:HIS39 4.7 60.4 1.0
CA B:CYS16 4.8 50.0 1.0

Zinc binding site 5 out of 6 in 5rmh

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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 Z1101755952


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 Z1101755952 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:0.1
occ:1.00
 SG B:CYS26 2.2 89.4 1.0
SG B:CYS5 2.4 88.1 1.0
SG B:CYS29 2.5 90.8 1.0
CB B:CYS8 2.7 0.1 1.0
CB B:CYS29 3.1 83.5 1.0
CB B:CYS26 3.2 90.2 1.0
SG B:CYS8 3.4 0.8 1.0
CB B:CYS5 3.5 96.4 1.0
N B:CYS26 3.6 87.4 1.0
N B:CYS8 3.7 0.3 1.0
CA B:CYS8 3.8 0.6 1.0
CA B:CYS26 3.9 86.7 1.0
N B:CYS29 4.1 82.2 1.0
CA B:CYS29 4.2 77.5 1.0
CB B:LEU7 4.5 0.1 1.0
C B:LEU7 4.6 0.9 1.0
O B:CYS26 4.6 83.6 1.0
OG B:SER10 4.6 85.8 1.0
C B:CYS26 4.6 85.3 1.0
CB B:SER10 4.7 90.6 1.0
C B:CYS8 4.8 0.5 1.0
C B:LEU25 4.8 83.2 1.0
CA B:LEU7 4.9 98.0 1.0
N B:GLY99 4.9 96.0 1.0
CA B:CYS5 4.9 94.5 1.0
N B:LEU7 4.9 95.8 1.0
CA B:GLY99 5.0 92.7 1.0

Zinc binding site 6 out of 6 in 5rmh

Go back to Zinc Binding Sites List in 5rmh
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1101755952


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 Z1101755952 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:0.4
occ:1.00
 SG B:CYS50 2.3 92.3 1.0
SG B:CYS55 2.3 0.4 1.0
ND1 B:HIS75 2.3 99.1 1.0
SG B:CYS72 3.0 94.2 1.0
CE1 B:HIS75 3.2 99.0 1.0
CB B:CYS50 3.3 0.0 1.0
CB B:CYS55 3.3 0.6 1.0
CG B:HIS75 3.4 99.0 1.0
CB B:CYS72 3.5 92.9 1.0
CB B:HIS75 3.7 99.5 1.0
N B:CYS72 3.9 92.9 1.0
CA B:CYS72 4.3 92.9 1.0
CB B:ALA52 4.3 0.2 1.0
CG2 B:VAL57 4.4 0.5 1.0
NE2 B:HIS75 4.4 99.6 1.0
CD2 B:HIS75 4.5 99.0 1.0
N B:HIS75 4.5 95.8 1.0
CB B:VAL57 4.6 0.1 1.0
CA B:CYS50 4.7 0.3 1.0
CA B:CYS55 4.7 1.0 1.0
CA B:HIS75 4.8 0.5 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 04:23:18 2024

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