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Zinc in PDB 5rmg: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z285675722

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z285675722

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z285675722:
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 Z285675722, PDB code: 5rmg 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) 81.29 / 2.12
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.031, 70.146, 85.409, 103.02, 96.17, 112.22
R / Rfree (%) 17 / 25.6

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 Z285675722 (pdb code 5rmg). 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 Z285675722, PDB code: 5rmg:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmg

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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 Z285675722


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 Z285675722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:70.1
occ:1.00
 SG A:CYS50 2.2 73.4 1.0
ND1 A:HIS75 2.4 66.7 1.0
SG A:CYS55 2.4 76.7 1.0
SG A:CYS72 2.7 69.5 1.0
CB A:CYS50 3.2 76.2 1.0
CG A:HIS75 3.3 64.5 1.0
CE1 A:HIS75 3.3 65.7 1.0
CB A:CYS72 3.4 69.5 1.0
CB A:CYS55 3.5 80.6 1.0
CB A:HIS75 3.6 63.5 1.0
N A:CYS72 3.7 67.6 1.0
CA A:CYS72 4.1 69.7 1.0
CB A:ALA52 4.2 66.1 1.0
CG2 A:VAL57 4.4 74.0 1.0
CD2 A:HIS75 4.4 64.6 1.0
NE2 A:HIS75 4.4 63.1 1.0
N A:HIS75 4.5 68.1 1.0
CA A:CYS50 4.6 75.8 1.0
CB A:VAL57 4.6 78.7 1.0
CA A:HIS75 4.7 66.4 1.0
C A:TYR71 4.9 65.5 1.0
CA A:CYS55 4.9 83.1 1.0
C A:CYS72 4.9 71.7 1.0

Zinc binding site 2 out of 6 in 5rmg

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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 Z285675722


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 Z285675722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.1
occ:1.00
 NE2 A:HIS33 2.0 67.5 1.0
ND1 A:HIS39 2.0 74.9 1.0
SG A:CYS16 2.3 0.3 1.0
SG A:CYS19 2.5 76.4 1.0
CE1 A:HIS33 2.9 69.7 1.0
CD2 A:HIS33 3.0 71.2 1.0
CE1 A:HIS39 3.0 77.2 1.0
CG A:HIS39 3.1 79.2 1.0
CB A:HIS39 3.4 76.9 1.0
N A:CYS19 3.5 74.5 1.0
CB A:CYS19 3.5 73.7 1.0
CB A:CYS16 3.6 0.9 1.0
CA A:CYS19 3.8 78.2 1.0
ND1 A:HIS33 4.1 71.5 1.0
CG A:HIS33 4.1 72.8 1.0
NE2 A:HIS39 4.2 82.2 1.0
C A:ALA18 4.2 81.2 1.0
CD2 A:HIS39 4.2 81.3 1.0
CB A:ALA110 4.4 74.9 1.0
CB A:ALA18 4.4 85.6 1.0
CA A:ALA18 4.6 84.5 1.0
N A:ALA18 4.8 83.8 1.0
CA A:CYS16 4.8 99.7 1.0
CA A:HIS39 4.9 75.9 1.0
O A:ALA18 4.9 81.1 1.0
CE2 A:PHE106 5.0 78.4 1.0

Zinc binding site 3 out of 6 in 5rmg

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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 Z285675722


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 Z285675722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.8
occ:1.00
 SG A:CYS5 2.2 0.6 1.0
SG A:CYS29 2.4 0.9 1.0
SG A:CYS26 2.4 0.2 1.0
SG A:CYS8 3.0 0.6 1.0
CB A:CYS29 3.2 0.6 1.0
CB A:CYS26 3.3 0.5 1.0
CB A:CYS5 3.4 0.9 1.0
CB A:CYS8 3.4 0.8 1.0
N A:CYS8 3.4 0.5 1.0
N A:CYS26 3.7 0.9 1.0
CA A:CYS8 3.9 0.5 1.0
CA A:CYS26 4.0 0.6 1.0
CB A:LEU7 4.3 0.1 1.0
C A:LEU7 4.5 0.7 1.0
N A:CYS29 4.5 0.0 1.0
CA A:CYS29 4.5 98.5 1.0
C A:CYS8 4.5 0.4 1.0
N A:ASN9 4.7 0.4 1.0
CA A:LEU7 4.7 0.6 1.0
N A:LEU7 4.7 0.3 1.0
CA A:CYS5 4.7 0.1 1.0
C A:CYS26 4.8 0.9 1.0
C A:LEU25 4.9 0.3 1.0
N A:SER10 5.0 0.5 1.0
CB A:SER10 5.0 0.1 1.0

Zinc binding site 4 out of 6 in 5rmg

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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 Z285675722


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 Z285675722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:46.0
occ:1.00
 NE2 B:HIS33 2.0 55.0 1.0
ND1 B:HIS39 2.2 48.0 1.0
SG B:CYS16 2.2 53.3 1.0
SG B:CYS19 2.6 61.4 1.0
CD2 B:HIS33 3.0 56.4 1.0
CE1 B:HIS33 3.0 54.9 1.0
CE1 B:HIS39 3.1 50.1 1.0
CG B:HIS39 3.1 54.0 1.0
CB B:CYS19 3.4 62.6 1.0
N B:CYS19 3.4 61.0 1.0
CB B:HIS39 3.4 57.3 1.0
CB B:CYS16 3.5 59.5 1.0
CA B:CYS19 3.7 62.9 1.0
CG B:HIS33 4.1 56.6 1.0
C B:ALA18 4.1 58.3 1.0
ND1 B:HIS33 4.2 54.1 1.0
NE2 B:HIS39 4.3 53.5 1.0
CD2 B:HIS39 4.3 54.3 1.0
CB B:ALA18 4.4 53.4 1.0
CB B:ALA110 4.5 58.2 1.0
CA B:ALA18 4.6 57.0 1.0
N B:ALA18 4.6 61.1 1.0
CA B:CYS16 4.7 56.5 1.0
CA B:HIS39 4.9 59.1 1.0
O B:ALA18 4.9 57.2 1.0
C B:CYS16 4.9 58.1 1.0

Zinc binding site 5 out of 6 in 5rmg

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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 Z285675722


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 Z285675722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:88.2
occ:1.00
 SG B:CYS29 2.4 78.2 1.0
SG B:CYS26 2.5 82.7 1.0
SG B:CYS5 2.5 84.0 1.0
CB B:CYS8 2.7 96.5 1.0
CB B:CYS29 3.0 69.9 1.0
SG B:CYS8 3.2 97.2 1.0
CB B:CYS26 3.5 78.6 1.0
CB B:CYS5 3.7 87.0 1.0
N B:CYS8 3.7 97.5 1.0
N B:CYS26 3.8 77.4 1.0
CA B:CYS8 3.8 95.8 1.0
CA B:CYS26 4.2 79.4 1.0
CA B:CYS29 4.2 68.1 1.0
N B:CYS29 4.2 68.4 1.0
CB B:LEU7 4.4 93.3 1.0
C B:LEU7 4.4 94.8 1.0
N B:GLY99 4.7 91.9 1.0
CA B:GLY99 4.7 89.8 1.0
OG B:SER10 4.8 87.2 1.0
CA B:LEU7 4.8 91.7 1.0
CB B:SER10 4.8 90.5 1.0
N B:LEU7 4.8 86.8 1.0
C B:CYS26 4.9 81.2 1.0
C B:CYS8 4.9 96.1 1.0
C B:LEU25 5.0 73.8 1.0

Zinc binding site 6 out of 6 in 5rmg

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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 Z285675722


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 Z285675722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:0.4
occ:1.00
 SG B:CYS50 2.2 0.8 1.0
ND1 B:HIS75 2.4 0.6 1.0
SG B:CYS55 2.5 0.0 1.0
SG B:CYS72 2.9 0.7 1.0
CB B:CYS50 3.1 0.9 1.0
CB B:CYS55 3.2 0.7 1.0
CE1 B:HIS75 3.3 99.7 1.0
CG B:HIS75 3.3 98.8 1.0
CB B:CYS72 3.5 90.1 1.0
CB B:HIS75 3.6 96.8 1.0
N B:CYS72 3.9 88.0 1.0
CB B:ALA52 4.1 0.2 1.0
CA B:CYS72 4.3 91.2 1.0
CG2 B:VAL57 4.4 97.7 1.0
NE2 B:HIS75 4.4 0.4 1.0
CD2 B:HIS75 4.4 0.4 1.0
CA B:CYS50 4.5 0.6 1.0
CB B:VAL57 4.6 0.8 1.0
N B:HIS75 4.6 95.1 1.0
CA B:CYS55 4.7 0.6 1.0
CA B:HIS75 4.8 96.6 1.0
N B:ALA52 5.0 0.2 1.0
C B:TYR71 5.0 90.5 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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