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Zinc in PDB 5rmc: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z24758179

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z24758179

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z24758179:
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 Z24758179, PDB code: 5rmc 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) 81.63 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.219, 70.236, 85.632, 102.52, 96.43, 112.39
R / Rfree (%) 20.9 / 25.8

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 Z24758179 (pdb code 5rmc). 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 Z24758179, PDB code: 5rmc:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmc

Go back to Zinc Binding Sites List in 5rmc
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:55.2
occ:1.00
 ND1 A:HIS75 2.2 55.9 1.0
SG A:CYS50 2.3 58.9 1.0
SG A:CYS55 2.3 52.7 1.0
SG A:CYS72 2.6 57.9 1.0
CB A:CYS50 3.2 62.1 1.0
CE1 A:HIS75 3.2 59.6 1.0
CB A:CYS72 3.2 60.1 1.0
CG A:HIS75 3.2 51.6 1.0
CB A:CYS55 3.3 58.0 1.0
CB A:HIS75 3.5 53.9 1.0
N A:CYS72 3.7 57.8 1.0
CA A:CYS72 4.0 60.6 1.0
NE2 A:HIS75 4.3 55.0 1.0
CD2 A:HIS75 4.3 50.9 1.0
CB A:ALA52 4.4 59.3 1.0
CG2 A:VAL57 4.5 64.1 1.0
N A:HIS75 4.6 56.5 1.0
CA A:CYS50 4.6 57.9 1.0
CB A:VAL57 4.7 64.9 1.0
CA A:HIS75 4.7 53.6 1.0
C A:CYS72 4.7 64.9 1.0
CA A:CYS55 4.8 62.6 1.0
C A:TYR71 4.9 54.2 1.0

Zinc binding site 2 out of 6 in 5rmc

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:57.9
occ:1.00
 NE2 A:HIS33 1.9 33.0 1.0
ND1 A:HIS39 2.1 80.1 1.0
SG A:CYS16 2.2 88.4 1.0
SG A:CYS19 2.4 58.2 1.0
CE1 A:HIS33 2.8 39.6 1.0
CD2 A:HIS33 2.9 40.7 1.0
CG A:HIS39 3.1 80.8 1.0
CE1 A:HIS39 3.1 80.9 1.0
N A:CYS19 3.2 66.7 1.0
CB A:CYS16 3.3 80.8 1.0
CB A:HIS39 3.4 74.3 1.0
CB A:CYS19 3.5 49.3 1.0
CA A:CYS19 3.7 58.8 1.0
ND1 A:HIS33 3.9 42.4 1.0
CG A:HIS33 4.0 45.2 1.0
C A:ALA18 4.1 77.4 1.0
NE2 A:HIS39 4.2 78.8 1.0
CD2 A:HIS39 4.2 83.9 1.0
CB A:ALA18 4.4 85.0 1.0
CB A:ALA110 4.5 60.5 1.0
CA A:ALA18 4.6 81.1 1.0
CA A:CYS16 4.7 81.1 1.0
N A:ALA18 4.7 76.5 1.0
CA A:HIS39 4.9 70.1 1.0
CE2 A:PHE106 4.9 53.3 1.0
CZ A:PHE106 4.9 54.5 1.0

Zinc binding site 3 out of 6 in 5rmc

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.6
occ:1.00
 SG A:CYS5 2.0 91.7 1.0
SG A:CYS8 2.1 0.1 1.0
SG A:CYS29 2.6 87.5 1.0
SG A:CYS26 2.6 89.5 1.0
CB A:CYS5 3.1 92.2 1.0
CB A:CYS29 3.3 94.0 1.0
CB A:CYS26 3.4 86.0 1.0
CB A:CYS8 3.5 0.3 1.0
N A:CYS8 3.6 0.0 1.0
N A:CYS26 3.9 82.5 1.0
CA A:CYS8 4.0 0.9 1.0
CA A:CYS26 4.2 86.4 1.0
CB A:LEU7 4.3 98.2 1.0
C A:CYS8 4.5 1.0 1.0
C A:LEU7 4.5 96.7 1.0
CA A:CYS5 4.5 94.7 1.0
CA A:CYS29 4.5 91.3 1.0
N A:CYS29 4.6 94.5 1.0
CB A:SER10 4.6 98.2 1.0
N A:LEU7 4.7 84.2 1.0
CA A:LEU7 4.7 93.4 1.0
N A:ASN9 4.7 0.2 1.0
O A:CYS26 4.7 89.8 1.0
C A:CYS26 4.9 90.9 1.0
C A:CYS5 4.9 94.3 1.0
OG A:SER10 4.9 92.0 1.0
N A:SER10 4.9 0.7 1.0

Zinc binding site 4 out of 6 in 5rmc

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:40.6
occ:1.00
 NE2 B:HIS33 2.0 37.4 1.0
ND1 B:HIS39 2.1 54.8 1.0
SG B:CYS16 2.2 45.5 1.0
SG B:CYS19 2.4 42.6 1.0
CD2 B:HIS33 3.0 34.4 1.0
CE1 B:HIS33 3.0 38.2 1.0
CG B:HIS39 3.1 56.7 1.0
CE1 B:HIS39 3.1 54.8 1.0
CB B:HIS39 3.3 52.0 1.0
CB B:CYS16 3.4 50.0 1.0
CB B:CYS19 3.4 40.6 1.0
N B:CYS19 3.5 49.5 1.0
CA B:CYS19 3.8 44.7 1.0
CG B:HIS33 4.1 38.3 1.0
ND1 B:HIS33 4.1 34.9 1.0
NE2 B:HIS39 4.2 55.4 1.0
CD2 B:HIS39 4.2 54.8 1.0
C B:ALA18 4.3 48.5 1.0
CB B:ALA18 4.5 44.1 1.0
CB B:ALA110 4.5 40.0 1.0
CA B:CYS16 4.7 50.1 1.0
CA B:ALA18 4.8 46.6 1.0
CA B:HIS39 4.8 49.1 1.0
N B:ALA18 4.9 47.4 1.0
CE2 B:PHE106 4.9 38.0 1.0
CZ B:PHE106 5.0 40.3 1.0

Zinc binding site 5 out of 6 in 5rmc

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:60.2
occ:1.00
 SG B:CYS5 2.3 61.6 1.0
SG B:CYS29 2.4 50.1 1.0
SG B:CYS26 2.4 60.8 1.0
CB B:CYS29 2.9 47.5 1.0
CB B:CYS8 2.9 78.3 1.0
SG B:CYS8 3.1 94.6 1.0
CB B:CYS5 3.4 69.4 1.0
CB B:CYS26 3.5 58.7 1.0
N B:CYS26 3.9 64.1 1.0
N B:CYS8 3.9 76.2 1.0
N B:CYS29 4.0 48.9 1.0
CA B:CYS8 4.0 78.2 1.0
CA B:CYS29 4.0 47.3 1.0
CA B:CYS26 4.3 64.8 1.0
CB B:LEU7 4.5 82.4 1.0
C B:LEU7 4.6 76.6 1.0
CB B:SER10 4.7 71.8 1.0
CA B:GLY99 4.7 65.3 1.0
N B:GLY99 4.7 67.0 1.0
O B:CYS26 4.7 63.1 1.0
OG B:SER10 4.8 72.3 1.0
C B:CYS26 4.9 68.1 1.0
CA B:CYS5 4.9 70.6 1.0
CA B:LEU7 5.0 78.7 1.0

Zinc binding site 6 out of 6 in 5rmc

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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 Z24758179


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 Z24758179 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:83.4
occ:1.00
 SG B:CYS50 2.2 73.0 1.0
SG B:CYS55 2.3 83.3 1.0
ND1 B:HIS75 2.4 93.5 1.0
SG B:CYS72 2.8 67.8 1.0
CB B:CYS50 3.0 78.6 1.0
CB B:CYS55 3.2 89.5 1.0
CG B:HIS75 3.3 94.7 1.0
CE1 B:HIS75 3.4 92.8 1.0
CB B:CYS72 3.4 72.5 1.0
CB B:HIS75 3.5 91.7 1.0
N B:CYS72 3.8 67.7 1.0
CB B:ALA52 4.2 94.2 1.0
CA B:CYS72 4.2 74.1 1.0
CG2 B:VAL57 4.4 96.4 1.0
CA B:CYS50 4.4 81.2 1.0
CD2 B:HIS75 4.5 93.7 1.0
NE2 B:HIS75 4.5 91.4 1.0
N B:HIS75 4.6 77.7 1.0
CA B:CYS55 4.6 93.6 1.0
CB B:VAL57 4.6 95.8 1.0
CA B:HIS75 4.7 88.3 1.0
C B:CYS72 4.9 77.8 1.0
C B:TYR71 4.9 70.1 1.0
C B:CYS50 5.0 87.5 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 04:23:17 2024

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