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Zinc in PDB 5rm9: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434942

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434942

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434942:
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 Z2856434942, PDB code: 5rm9 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) 62.11 / 2.08
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.092, 70.011, 85.779, 102.72, 96.48, 112.21
R / Rfree (%) 16.7 / 25.4

Other elements in 5rm9:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434942 also contains other interesting chemical elements:

Fluorine (F) 1 atom

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 Z2856434942 (pdb code 5rm9). 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 Z2856434942, PDB code: 5rm9:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm9

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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 Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:78.2
occ:1.00
 SG A:CYS50 2.3 81.3 1.0
SG A:CYS55 2.3 95.6 1.0
ND1 A:HIS75 2.6 79.0 1.0
SG A:CYS72 2.7 79.8 1.0
CB A:CYS55 3.2 94.7 1.0
CB A:CYS50 3.2 85.8 1.0
CB A:CYS72 3.4 81.4 1.0
CG A:HIS75 3.4 77.9 1.0
CB A:HIS75 3.6 74.5 1.0
CE1 A:HIS75 3.6 77.5 1.0
N A:CYS72 3.8 76.5 1.0
CB A:ALA52 4.1 73.8 1.0
CA A:CYS72 4.2 79.1 1.0
N A:HIS75 4.4 79.4 1.0
CG2 A:VAL57 4.6 76.5 1.0
CD2 A:HIS75 4.6 77.1 1.0
CA A:HIS75 4.6 76.5 1.0
CA A:CYS55 4.6 96.1 1.0
CA A:CYS50 4.7 80.3 1.0
NE2 A:HIS75 4.7 75.8 1.0
CB A:VAL57 4.7 82.1 1.0
C A:CYS72 4.9 83.7 1.0
C A:TYR71 4.9 74.5 1.0

Zinc binding site 2 out of 6 in 5rm9

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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 Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:74.0
occ:1.00
 NE2 A:HIS33 2.1 61.6 1.0
ND1 A:HIS39 2.2 92.1 1.0
SG A:CYS16 2.3 94.2 1.0
SG A:CYS19 2.4 81.6 1.0
CD2 A:HIS33 3.0 67.8 1.0
CE1 A:HIS33 3.1 64.8 1.0
CE1 A:HIS39 3.1 93.9 1.0
CG A:HIS39 3.2 92.6 1.0
CB A:CYS19 3.3 75.2 1.0
CB A:CYS16 3.4 92.8 1.0
N A:CYS19 3.4 73.8 1.0
CB A:HIS39 3.5 85.7 1.0
CA A:CYS19 3.6 76.7 1.0
C A:ALA18 4.0 75.3 1.0
CG A:HIS33 4.2 69.9 1.0
ND1 A:HIS33 4.2 67.7 1.0
CB A:ALA110 4.3 70.1 1.0
NE2 A:HIS39 4.3 95.9 1.0
CD2 A:HIS39 4.3 94.6 1.0
CB A:ALA18 4.4 80.7 1.0
O A:ALA18 4.6 73.7 1.0
CA A:ALA18 4.6 78.8 1.0
CA A:CYS16 4.7 93.6 1.0
N A:ALA18 4.8 79.0 1.0
CE2 A:PHE106 4.9 78.9 1.0
CZ A:PHE106 4.9 80.0 1.0
CA A:HIS39 5.0 82.3 1.0

Zinc binding site 3 out of 6 in 5rm9

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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 Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.2
occ:1.00
 SG A:CYS8 2.3 0.6 1.0
SG A:CYS29 2.3 0.1 1.0
SG A:CYS5 2.5 0.7 1.0
SG A:CYS26 2.7 0.1 1.0
CB A:CYS29 2.9 0.1 1.0
CB A:CYS8 3.2 0.7 1.0
CB A:CYS26 3.5 0.6 1.0
N A:CYS8 3.6 0.1 1.0
CB A:CYS5 3.7 0.0 1.0
CA A:CYS8 4.0 0.5 1.0
N A:CYS26 4.0 0.6 1.0
CB A:LEU7 4.1 0.1 1.0
CA A:CYS29 4.2 0.4 1.0
CA A:CYS26 4.3 0.6 1.0
C A:LEU7 4.3 0.8 1.0
N A:CYS29 4.4 0.3 1.0
CA A:LEU7 4.6 0.4 1.0
N A:LEU7 4.8 0.3 1.0
OG A:SER10 4.9 0.0 1.0
C A:CYS8 4.9 0.0 1.0
C A:CYS26 5.0 0.5 1.0

Zinc binding site 4 out of 6 in 5rm9

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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 Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:61.2
occ:1.00
 NE2 B:HIS33 1.9 67.2 1.0
ND1 B:HIS39 2.1 59.6 1.0
SG B:CYS16 2.3 65.3 1.0
SG B:CYS19 2.7 69.1 1.0
CD2 B:HIS33 2.9 65.6 1.0
CE1 B:HIS33 3.0 67.2 1.0
CG B:HIS39 3.0 63.8 1.0
CE1 B:HIS39 3.1 61.0 1.0
CB B:HIS39 3.3 63.6 1.0
CB B:CYS16 3.4 71.0 1.0
CB B:CYS19 3.5 67.1 1.0
N B:CYS19 3.5 64.8 1.0
CA B:CYS19 3.7 67.2 1.0
CG B:HIS33 4.1 64.6 1.0
ND1 B:HIS33 4.1 64.2 1.0
CD2 B:HIS39 4.2 61.5 1.0
C B:ALA18 4.2 64.4 1.0
NE2 B:HIS39 4.2 61.7 1.0
CB B:ALA110 4.4 56.0 1.0
CB B:ALA18 4.5 62.9 1.0
CA B:ALA18 4.7 65.3 1.0
CA B:HIS39 4.8 66.5 1.0
CA B:CYS16 4.8 69.4 1.0
N B:ALA18 4.8 67.3 1.0
O B:ALA18 4.9 63.6 1.0

Zinc binding site 5 out of 6 in 5rm9

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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 Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:87.5
occ:1.00
 SG B:CYS5 2.3 80.8 1.0
SG B:CYS26 2.3 87.8 1.0
SG B:CYS29 2.5 85.0 1.0
CB B:CYS8 2.9 0.9 1.0
CB B:CYS29 3.1 74.9 1.0
CB B:CYS5 3.5 91.5 1.0
CB B:CYS26 3.5 85.1 1.0
N B:CYS8 3.7 96.2 1.0
SG B:CYS8 3.7 0.8 1.0
CA B:CYS8 3.9 98.5 1.0
N B:CYS26 3.9 82.1 1.0
N B:CYS29 4.2 76.1 1.0
CA B:CYS29 4.2 73.4 1.0
CA B:CYS26 4.3 83.5 1.0
CB B:LEU7 4.4 88.3 1.0
C B:LEU7 4.5 92.2 1.0
N B:GLY99 4.5 97.5 1.0
OG B:SER10 4.6 92.1 1.0
CA B:GLY99 4.6 97.8 1.0
C B:CYS8 4.7 99.0 1.0
CA B:LEU7 4.8 89.8 1.0
N B:LEU7 4.9 90.1 1.0
CA B:CYS5 4.9 91.1 1.0
CB B:SER10 4.9 92.1 1.0
C B:CYS26 5.0 85.9 1.0
N B:ASN9 5.0 99.3 1.0

Zinc binding site 6 out of 6 in 5rm9

Go back to Zinc Binding Sites List in 5rm9
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2856434942


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 Z2856434942 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:99.4
occ:1.00
 SG B:CYS50 2.2 91.5 1.0
SG B:CYS55 2.4 0.6 1.0
ND1 B:HIS75 2.6 0.5 1.0
SG B:CYS72 2.8 94.2 1.0
CB B:CYS50 3.1 0.5 1.0
CB B:CYS55 3.2 0.5 1.0
CB B:CYS72 3.4 93.9 1.0
CG B:HIS75 3.5 0.0 1.0
CB B:HIS75 3.5 0.6 1.0
CE1 B:HIS75 3.7 0.7 1.0
N B:CYS72 3.8 95.0 1.0
CB B:ALA52 4.0 0.3 1.0
CA B:CYS72 4.2 96.0 1.0
N B:HIS75 4.4 0.1 1.0
CA B:CYS50 4.6 0.3 1.0
CG2 B:VAL57 4.6 0.1 1.0
CA B:HIS75 4.6 0.6 1.0
CA B:CYS55 4.6 0.6 1.0
CD2 B:HIS75 4.7 0.1 1.0
CB B:VAL57 4.7 0.1 1.0
NE2 B:HIS75 4.8 0.6 1.0
C B:TYR71 4.9 95.7 1.0
C B:CYS72 4.9 97.4 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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