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Zinc in PDB 5rm6: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540:
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 Z396380540, PDB code: 5rm6 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) 81.58 / 2.13
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.116, 70.245, 85.683, 102.81, 96.39, 112.15
R / Rfree (%) 16.2 / 25.1

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 Z396380540 (pdb code 5rm6). 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 Z396380540, PDB code: 5rm6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm6

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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 Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:48.9
occ:1.00
 SG A:CYS50 2.4 59.5 1.0
SG A:CYS72 2.5 42.7 1.0
ND1 A:HIS75 2.5 69.3 1.0
SG A:CYS55 2.5 77.9 1.0
CB A:CYS72 3.1 50.7 1.0
CB A:CYS50 3.2 69.5 1.0
CG A:HIS75 3.4 67.1 1.0
CB A:HIS75 3.4 67.8 1.0
N A:CYS72 3.5 55.7 1.0
CE1 A:HIS75 3.6 66.7 1.0
CB A:CYS55 3.6 78.8 1.0
CA A:CYS72 3.9 56.0 1.0
N A:HIS75 4.2 69.1 1.0
CG2 A:VAL57 4.4 75.2 1.0
CA A:HIS75 4.4 68.8 1.0
CB A:ALA52 4.5 63.7 1.0
CD2 A:HIS75 4.6 65.1 1.0
CB A:VAL57 4.6 76.5 1.0
C A:TYR71 4.6 57.4 1.0
C A:CYS72 4.6 62.6 1.0
CA A:CYS50 4.7 69.4 1.0
NE2 A:HIS75 4.7 65.5 1.0
CA A:TYR71 4.9 58.2 1.0
CB A:SER74 5.0 70.0 1.0
O A:CYS72 5.0 65.5 1.0

Zinc binding site 2 out of 6 in 5rm6

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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 Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:72.4
occ:1.00
 NE2 A:HIS33 1.9 71.2 1.0
ND1 A:HIS39 2.2 81.7 1.0
SG A:CYS19 2.3 67.4 1.0
SG A:CYS16 2.4 97.1 1.0
CE1 A:HIS33 2.8 71.6 1.0
CD2 A:HIS33 3.0 72.6 1.0
CG A:HIS39 3.2 83.7 1.0
CE1 A:HIS39 3.2 83.4 1.0
CB A:HIS39 3.4 79.5 1.0
CB A:CYS16 3.4 95.2 1.0
CB A:CYS19 3.6 73.3 1.0
N A:CYS19 3.6 77.8 1.0
CA A:CYS19 3.9 78.5 1.0
ND1 A:HIS33 4.0 73.4 1.0
CG A:HIS33 4.1 74.1 1.0
C A:ALA18 4.2 83.8 1.0
CD2 A:HIS39 4.3 84.6 1.0
NE2 A:HIS39 4.3 84.3 1.0
CB A:ALA110 4.3 68.9 1.0
CB A:ALA18 4.5 86.0 1.0
CA A:ALA18 4.7 87.3 1.0
CA A:CYS16 4.8 95.6 1.0
CE2 A:PHE106 4.9 79.5 1.0
N A:ALA18 4.9 89.1 1.0
O A:ALA18 4.9 84.7 1.0
CA A:HIS39 4.9 76.9 1.0
CZ A:PHE106 5.0 81.9 1.0

Zinc binding site 3 out of 6 in 5rm6

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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 Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.4
occ:1.00
 SG A:CYS5 2.2 0.1 1.0
SG A:CYS8 2.4 0.0 1.0
SG A:CYS26 2.7 0.9 1.0
SG A:CYS29 2.7 0.6 1.0
CB A:CYS26 3.1 0.6 1.0
CB A:CYS5 3.3 0.1 1.0
CB A:CYS29 3.3 0.7 1.0
CB A:CYS8 3.4 0.1 1.0
N A:CYS8 3.4 0.9 1.0
N A:CYS26 3.8 0.9 1.0
CA A:CYS8 3.8 0.2 1.0
CA A:CYS26 4.0 0.2 1.0
C A:LEU7 4.2 0.6 1.0
CB A:LEU7 4.3 0.1 1.0
C A:CYS8 4.4 0.0 1.0
CA A:LEU7 4.6 0.8 1.0
CA A:CYS29 4.6 97.7 1.0
N A:LEU7 4.6 0.9 1.0
N A:CYS29 4.6 0.3 1.0
N A:ASN9 4.7 0.2 1.0
CA A:CYS5 4.7 0.4 1.0
CB A:SER10 4.7 0.6 1.0
C A:CYS26 4.8 0.5 1.0
OG A:SER10 4.9 98.8 1.0
N A:SER10 4.9 0.9 1.0
O A:CYS26 4.9 0.8 1.0
C A:LEU25 5.0 98.7 1.0
O A:CYS8 5.0 0.7 1.0

Zinc binding site 4 out of 6 in 5rm6

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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 Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:58.7
occ:1.00
 NE2 B:HIS33 2.0 57.7 1.0
ND1 B:HIS39 2.2 66.5 1.0
SG B:CYS16 2.2 65.7 1.0
SG B:CYS19 2.4 56.2 1.0
CE1 B:HIS33 3.0 57.9 1.0
CD2 B:HIS33 3.1 58.6 1.0
CG B:HIS39 3.1 67.5 1.0
CE1 B:HIS39 3.2 66.3 1.0
CB B:HIS39 3.3 66.4 1.0
CB B:CYS16 3.4 66.9 1.0
N B:CYS19 3.5 61.3 1.0
CB B:CYS19 3.6 57.3 1.0
CA B:CYS19 3.9 60.2 1.0
C B:ALA18 4.1 59.6 1.0
ND1 B:HIS33 4.1 58.4 1.0
CG B:HIS33 4.2 59.5 1.0
CD2 B:HIS39 4.3 67.3 1.0
NE2 B:HIS39 4.3 67.3 1.0
CB B:ALA18 4.4 53.6 1.0
CB B:ALA110 4.6 52.3 1.0
CA B:ALA18 4.6 58.7 1.0
N B:ALA18 4.7 61.2 1.0
CA B:CYS16 4.7 66.8 1.0
CA B:HIS39 4.8 64.8 1.0
O B:ALA18 4.8 63.6 1.0

Zinc binding site 5 out of 6 in 5rm6

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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 Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:95.1
occ:1.00
 SG B:CYS26 2.2 82.2 1.0
SG B:CYS5 2.2 78.3 1.0
SG B:CYS29 2.7 76.9 1.0
CB B:CYS8 2.7 0.3 1.0
CB B:CYS29 3.1 75.2 1.0
CB B:CYS26 3.3 82.0 1.0
CB B:CYS5 3.3 86.4 1.0
SG B:CYS8 3.5 0.6 1.0
N B:CYS8 3.6 0.0 1.0
N B:CYS26 3.7 77.6 1.0
CA B:CYS8 3.8 98.6 1.0
CA B:CYS26 4.1 79.8 1.0
N B:CYS29 4.2 76.7 1.0
CA B:CYS29 4.3 73.2 1.0
C B:LEU7 4.4 96.7 1.0
CB B:LEU7 4.5 91.8 1.0
CB B:SER10 4.6 87.5 1.0
C B:CYS8 4.6 99.4 1.0
OG B:SER10 4.6 84.0 1.0
CA B:CYS5 4.8 86.4 1.0
N B:LEU7 4.8 88.6 1.0
CA B:LEU7 4.8 92.7 1.0
N B:ASN9 4.9 98.3 1.0
C B:LEU25 4.9 76.1 1.0
C B:CYS26 4.9 82.2 1.0
N B:GLY99 4.9 95.8 1.0
N B:SER10 5.0 91.6 1.0

Zinc binding site 6 out of 6 in 5rm6

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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 Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:0.7
occ:1.00
 SG B:CYS50 2.2 0.4 1.0
SG B:CYS55 2.4 0.3 1.0
ND1 B:HIS75 2.5 0.9 1.0
SG B:CYS72 2.8 94.7 1.0
CB B:CYS50 3.0 0.8 1.0
CB B:CYS72 3.3 89.4 1.0
CB B:CYS55 3.4 0.1 1.0
CG B:HIS75 3.4 0.6 1.0
CB B:HIS75 3.5 99.7 1.0
N B:CYS72 3.6 90.3 1.0
CE1 B:HIS75 3.6 0.0 1.0
CA B:CYS72 4.0 91.2 1.0
CB B:ALA52 4.3 0.7 1.0
N B:HIS75 4.4 96.2 1.0
CA B:CYS50 4.5 0.3 1.0
CG2 B:VAL57 4.5 96.9 1.0
CA B:HIS75 4.6 97.0 1.0
CB B:VAL57 4.6 97.6 1.0
CD2 B:HIS75 4.6 0.2 1.0
NE2 B:HIS75 4.7 0.0 1.0
C B:TYR71 4.7 89.4 1.0
CA B:CYS55 4.8 0.4 1.0
C B:CYS72 4.9 92.1 1.0
CA B:TYR71 4.9 93.6 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 04:17:42 2024

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