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Zinc in PDB 5rmk: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1273312153:
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 Z1273312153, PDB code: 5rmk 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) 81.32 / 2.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.034, 70.039, 85.317, 102.81, 96.07, 112.42
R / Rfree (%) 22.2 / 27.4

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 Z1273312153 (pdb code 5rmk). 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 Z1273312153, PDB code: 5rmk:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmk

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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 Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:59.2
occ:1.00
 ND1 A:HIS75 2.3 49.0 1.0
SG A:CYS50 2.3 55.3 1.0
SG A:CYS55 2.3 62.2 1.0
SG A:CYS72 2.6 55.1 1.0
CE1 A:HIS75 3.2 51.8 1.0
CB A:CYS50 3.2 61.0 1.0
CB A:CYS72 3.3 58.3 1.0
CG A:HIS75 3.3 45.8 1.0
CB A:CYS55 3.3 55.4 1.0
CB A:HIS75 3.6 45.7 1.0
N A:CYS72 3.7 53.1 1.0
CA A:CYS72 4.1 59.6 1.0
CB A:ALA52 4.2 54.2 1.0
NE2 A:HIS75 4.4 46.7 1.0
CG2 A:VAL57 4.4 69.2 1.0
CD2 A:HIS75 4.4 47.5 1.0
N A:HIS75 4.6 53.6 1.0
CB A:VAL57 4.6 67.2 1.0
CA A:CYS50 4.7 59.9 1.0
CA A:HIS75 4.7 47.7 1.0
CA A:CYS55 4.7 58.1 1.0
C A:CYS72 4.8 66.1 1.0
C A:TYR71 4.9 47.5 1.0
O A:CYS72 4.9 63.9 1.0
CB A:SER74 5.0 56.0 1.0

Zinc binding site 2 out of 6 in 5rmk

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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 Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:53.3
occ:1.00
 NE2 A:HIS33 1.9 40.2 1.0
ND1 A:HIS39 2.2 63.0 1.0
SG A:CYS16 2.2 67.4 1.0
SG A:CYS19 2.5 53.4 1.0
CD2 A:HIS33 2.9 47.2 1.0
CE1 A:HIS33 2.9 47.9 1.0
CG A:HIS39 3.1 70.9 1.0
CE1 A:HIS39 3.2 68.5 1.0
N A:CYS19 3.2 46.0 1.0
CB A:CYS16 3.3 70.2 1.0
CB A:HIS39 3.3 64.8 1.0
CB A:CYS19 3.5 47.3 1.0
CA A:CYS19 3.7 49.4 1.0
ND1 A:HIS33 4.0 51.3 1.0
CG A:HIS33 4.0 50.5 1.0
C A:ALA18 4.1 53.9 1.0
CD2 A:HIS39 4.2 71.1 1.0
NE2 A:HIS39 4.2 65.9 1.0
CB A:ALA18 4.3 60.3 1.0
CB A:ALA110 4.4 58.3 1.0
CA A:ALA18 4.6 60.3 1.0
CA A:CYS16 4.7 69.3 1.0
N A:ALA18 4.7 53.6 1.0
CE2 A:PHE106 4.8 53.4 1.0
CA A:HIS39 4.8 62.1 1.0
CZ A:PHE106 4.9 51.9 1.0
O A:ALA18 4.9 60.2 1.0

Zinc binding site 3 out of 6 in 5rmk

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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 Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:89.9
occ:1.00
 SG A:CYS29 2.2 81.0 1.0
SG A:CYS8 2.2 0.8 1.0
SG A:CYS5 2.5 64.2 1.0
SG A:CYS26 2.5 80.1 1.0
CB A:CYS29 3.2 84.5 1.0
CB A:CYS8 3.3 0.6 1.0
CB A:CYS26 3.3 84.5 1.0
CB A:CYS5 3.8 73.3 1.0
N A:CYS8 3.8 98.9 1.0
N A:CYS26 4.1 81.6 1.0
CA A:CYS8 4.1 0.5 1.0
CA A:CYS26 4.2 86.6 1.0
N A:CYS29 4.3 82.4 1.0
CA A:CYS29 4.3 82.7 1.0
CB A:LEU7 4.4 97.7 1.0
CB A:SER10 4.8 85.6 1.0
C A:CYS8 4.8 99.4 1.0
C A:LEU7 4.8 96.3 1.0
C A:CYS26 4.8 91.6 1.0
O A:CYS26 4.9 90.3 1.0
OG A:SER10 4.9 80.3 1.0

Zinc binding site 4 out of 6 in 5rmk

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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 Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:37.7
occ:1.00
 NE2 B:HIS33 1.9 32.0 1.0
ND1 B:HIS39 2.1 50.9 1.0
SG B:CYS16 2.2 45.7 1.0
SG B:CYS19 2.3 40.8 1.0
CD2 B:HIS33 2.9 32.2 1.0
CG B:HIS39 3.0 55.0 1.0
CE1 B:HIS33 3.0 33.5 1.0
CE1 B:HIS39 3.1 52.7 1.0
CB B:HIS39 3.2 50.2 1.0
CB B:CYS16 3.4 43.7 1.0
CB B:CYS19 3.4 41.1 1.0
N B:CYS19 3.5 50.5 1.0
CA B:CYS19 3.8 46.3 1.0
CG B:HIS33 4.1 36.0 1.0
ND1 B:HIS33 4.1 32.1 1.0
CD2 B:HIS39 4.1 51.6 1.0
NE2 B:HIS39 4.2 53.5 1.0
C B:ALA18 4.2 50.8 1.0
CB B:ALA18 4.5 45.6 1.0
CB B:ALA110 4.5 39.6 1.0
CA B:HIS39 4.7 47.2 1.0
CA B:CYS16 4.8 41.4 1.0
CA B:ALA18 4.8 47.7 1.0
N B:ALA18 4.9 46.9 1.0
CE2 B:PHE106 5.0 38.6 1.0

Zinc binding site 5 out of 6 in 5rmk

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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 Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:50.2
occ:1.00
 SG B:CYS29 2.2 44.1 1.0
SG B:CYS5 2.3 54.4 1.0
SG B:CYS26 2.4 54.9 1.0
CB B:CYS8 2.8 70.8 1.0
CB B:CYS29 3.0 45.7 1.0
SG B:CYS8 3.0 88.1 1.0
CB B:CYS5 3.3 60.6 1.0
CB B:CYS26 3.5 52.2 1.0
N B:CYS8 3.8 70.8 1.0
CA B:CYS8 3.9 72.7 1.0
N B:CYS26 3.9 58.2 1.0
N B:CYS29 4.1 46.1 1.0
CA B:CYS29 4.2 44.3 1.0
CA B:CYS26 4.3 54.4 1.0
CB B:LEU7 4.4 74.4 1.0
C B:LEU7 4.6 70.7 1.0
CA B:GLY99 4.7 67.4 1.0
N B:GLY99 4.7 67.9 1.0
OG B:SER10 4.7 62.6 1.0
CB B:SER10 4.7 59.4 1.0
CA B:CYS5 4.8 63.3 1.0
OG B:SER100 4.8 63.5 1.0
C B:CYS26 4.9 54.0 1.0
C B:CYS8 4.9 66.8 1.0
CA B:LEU7 4.9 68.9 1.0
N B:LEU7 4.9 59.6 1.0
O B:CYS26 5.0 50.4 1.0

Zinc binding site 6 out of 6 in 5rmk

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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 Z1273312153


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 Z1273312153 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:64.5
occ:1.00
 SG B:CYS50 2.2 58.5 1.0
ND1 B:HIS75 2.2 68.7 1.0
SG B:CYS55 2.3 64.0 1.0
SG B:CYS72 2.6 58.0 1.0
CG B:HIS75 3.2 69.4 1.0
CB B:CYS50 3.2 62.8 1.0
CE1 B:HIS75 3.2 72.2 1.0
CB B:CYS55 3.3 74.1 1.0
CB B:CYS72 3.3 59.7 1.0
CB B:HIS75 3.4 68.1 1.0
N B:CYS72 3.7 56.3 1.0
CB B:ALA52 3.9 78.6 1.0
CA B:CYS72 4.1 60.8 1.0
CD2 B:HIS75 4.3 72.9 1.0
NE2 B:HIS75 4.3 72.3 1.0
N B:HIS75 4.4 60.7 1.0
CG2 B:VAL57 4.5 78.4 1.0
CA B:HIS75 4.5 64.4 1.0
CA B:CYS50 4.6 68.9 1.0
C B:CYS72 4.7 63.9 1.0
CA B:CYS55 4.7 79.1 1.0
CB B:VAL57 4.7 80.1 1.0
O B:CYS72 4.8 57.9 1.0
C B:TYR71 4.9 58.1 1.0
C B:SER74 4.9 66.5 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 04:29:04 2024

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