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Zinc in PDB 5rmb: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434920

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434920

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434920:
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 Z2856434920, PDB code: 5rmb 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) 62.24 / 2.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.133, 70.222, 85.439, 102.98, 96.21, 112.22
R / Rfree (%) 16.5 / 24.9

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 Z2856434920 (pdb code 5rmb). 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 Z2856434920, PDB code: 5rmb:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmb

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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 Z2856434920


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 Z2856434920 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:72.6
occ:1.00
 SG A:CYS50 2.3 80.3 1.0
SG A:CYS55 2.3 80.3 1.0
ND1 A:HIS75 2.3 66.0 1.0
SG A:CYS72 2.7 69.2 1.0
CB A:CYS50 3.2 82.8 1.0
CE1 A:HIS75 3.3 65.7 1.0
CG A:HIS75 3.3 65.0 1.0
CB A:CYS55 3.4 83.6 1.0
CB A:CYS72 3.4 76.2 1.0
CB A:HIS75 3.6 64.0 1.0
N A:CYS72 3.8 74.7 1.0
CA A:CYS72 4.2 74.5 1.0
CB A:ALA52 4.2 70.9 1.0
CG2 A:VAL57 4.5 83.4 1.0
NE2 A:HIS75 4.5 64.8 1.0
CD2 A:HIS75 4.5 63.8 1.0
N A:HIS75 4.5 67.7 1.0
CB A:VAL57 4.6 86.4 1.0
CA A:CYS50 4.7 79.3 1.0
CA A:HIS75 4.7 66.6 1.0
CA A:CYS55 4.8 88.0 1.0
C A:TYR71 4.9 70.7 1.0
C A:CYS72 5.0 76.9 1.0

Zinc binding site 2 out of 6 in 5rmb

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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 Z2856434920


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 Z2856434920 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:76.8
occ:1.00
 NE2 A:HIS33 2.0 65.9 1.0
ND1 A:HIS39 2.1 92.0 1.0
SG A:CYS16 2.2 0.5 1.0
SG A:CYS19 2.5 78.4 1.0
CE1 A:HIS33 3.0 67.1 1.0
CG A:HIS39 3.1 92.0 1.0
CD2 A:HIS33 3.1 68.1 1.0
CE1 A:HIS39 3.1 91.4 1.0
CB A:HIS39 3.4 90.2 1.0
CB A:CYS16 3.4 98.8 1.0
CB A:CYS19 3.4 77.7 1.0
N A:CYS19 3.4 81.8 1.0
CA A:CYS19 3.7 84.4 1.0
ND1 A:HIS33 4.2 69.5 1.0
C A:ALA18 4.2 87.9 1.0
CG A:HIS33 4.2 71.9 1.0
CD2 A:HIS39 4.2 91.8 1.0
NE2 A:HIS39 4.2 90.3 1.0
CB A:ALA110 4.3 67.0 1.0
CB A:ALA18 4.4 91.0 1.0
CA A:ALA18 4.7 89.0 1.0
CA A:CYS16 4.8 96.8 1.0
N A:ALA18 4.8 90.2 1.0
CA A:HIS39 4.8 84.6 1.0
O A:ALA18 4.9 86.9 1.0
CE2 A:PHE106 5.0 82.3 1.0

Zinc binding site 3 out of 6 in 5rmb

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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 Z2856434920


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 Z2856434920 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.2
occ:1.00
 SG A:CYS26 2.3 0.7 1.0
SG A:CYS5 2.4 0.2 1.0
SG A:CYS29 2.5 0.4 1.0
SG A:CYS8 2.7 0.7 1.0
CB A:CYS29 3.1 0.3 1.0
CB A:CYS26 3.5 0.5 1.0
CB A:CYS8 3.5 0.9 1.0
N A:CYS8 3.6 0.0 1.0
CB A:CYS5 3.7 0.8 1.0
N A:CYS26 4.0 0.1 1.0
CA A:CYS8 4.0 0.2 1.0
CB A:LEU7 4.1 0.9 1.0
C A:LEU7 4.2 1.0 1.0
CA A:CYS26 4.3 0.9 1.0
CA A:CYS29 4.3 0.8 1.0
N A:CYS29 4.3 0.5 1.0
CA A:LEU7 4.6 0.3 1.0
N A:LEU7 4.7 0.8 1.0
C A:CYS8 4.7 0.7 1.0
OG A:SER10 4.8 0.2 1.0
CB A:SER10 5.0 0.8 1.0
N A:ASN9 5.0 0.5 1.0

Zinc binding site 4 out of 6 in 5rmb

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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 Z2856434920


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 Z2856434920 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:63.3
occ:1.00
 NE2 B:HIS33 1.9 60.5 1.0
ND1 B:HIS39 2.2 63.6 1.0
SG B:CYS16 2.2 67.7 1.0
SG B:CYS19 2.6 67.3 1.0
CD2 B:HIS33 2.9 59.7 1.0
CE1 B:HIS33 2.9 59.7 1.0
CG B:HIS39 3.1 66.7 1.0
CE1 B:HIS39 3.2 64.0 1.0
CB B:HIS39 3.3 68.9 1.0
CB B:CYS16 3.3 67.5 1.0
CB B:CYS19 3.5 68.9 1.0
N B:CYS19 3.6 68.6 1.0
CA B:CYS19 3.9 67.6 1.0
CG B:HIS33 4.1 60.5 1.0
ND1 B:HIS33 4.1 57.9 1.0
CD2 B:HIS39 4.3 64.9 1.0
C B:ALA18 4.3 64.4 1.0
NE2 B:HIS39 4.3 66.2 1.0
CB B:ALA110 4.4 58.9 1.0
CB B:ALA18 4.5 59.7 1.0
CA B:CYS16 4.7 67.4 1.0
CA B:ALA18 4.8 62.8 1.0
CA B:HIS39 4.8 69.0 1.0
N B:ALA18 4.8 63.1 1.0
CE2 B:PHE106 5.0 64.8 1.0

Zinc binding site 5 out of 6 in 5rmb

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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 Z2856434920


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 Z2856434920 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:93.8
occ:1.00
 SG B:CYS26 2.3 86.8 1.0
SG B:CYS5 2.4 90.1 1.0
SG B:CYS29 2.4 81.8 1.0
CB B:CYS8 2.8 96.0 1.0
CB B:CYS29 2.9 78.3 1.0
SG B:CYS8 3.1 96.3 1.0
CB B:CYS26 3.4 86.5 1.0
CB B:CYS5 3.7 93.6 1.0
N B:CYS8 3.7 92.5 1.0
CA B:CYS8 3.9 95.2 1.0
N B:CYS26 3.9 85.8 1.0
CA B:CYS29 4.1 76.7 1.0
N B:CYS29 4.2 78.7 1.0
CA B:CYS26 4.2 85.4 1.0
CB B:LEU7 4.3 86.7 1.0
C B:LEU7 4.4 89.0 1.0
N B:GLY99 4.7 94.8 1.0
CA B:LEU7 4.7 87.4 1.0
CA B:GLY99 4.8 92.8 1.0
OG B:SER10 4.8 82.2 1.0
N B:LEU7 4.8 83.8 1.0
C B:CYS26 5.0 86.6 1.0
C B:GLY99 5.0 89.6 1.0
C B:CYS8 5.0 96.1 1.0
CB B:SER10 5.0 86.9 1.0

Zinc binding site 6 out of 6 in 5rmb

Go back to Zinc Binding Sites List in 5rmb
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434920


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 Z2856434920 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:0.1
occ:1.00
 SG B:CYS50 2.2 87.7 1.0
SG B:CYS55 2.4 0.6 1.0
ND1 B:HIS75 2.4 0.8 1.0
SG B:CYS72 2.7 0.8 1.0
CB B:CYS50 3.1 0.5 1.0
CB B:CYS72 3.4 97.2 1.0
CG B:HIS75 3.4 0.0 1.0
CB B:CYS55 3.4 0.1 1.0
CE1 B:HIS75 3.4 0.0 1.0
CB B:HIS75 3.5 0.3 1.0
N B:CYS72 3.7 96.4 1.0
CA B:CYS72 4.1 97.9 1.0
CB B:ALA52 4.2 0.0 1.0
CG2 B:VAL57 4.5 0.9 1.0
N B:HIS75 4.5 98.4 1.0
CD2 B:HIS75 4.6 0.9 1.0
CA B:CYS50 4.6 0.7 1.0
NE2 B:HIS75 4.6 0.2 1.0
CB B:VAL57 4.6 1.0 1.0
CA B:HIS75 4.7 0.1 1.0
C B:TYR71 4.8 95.8 1.0
CA B:CYS55 4.8 0.2 1.0
C B:CYS72 4.9 99.1 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: Thu Aug 21 07:25:23 2025

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