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Zinc in PDB 5rmf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006:
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 Z54226006, PDB code: 5rmf 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) 81.49 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.190, 70.107, 85.386, 102.60, 96.01, 112.56
R / Rfree (%) 20.8 / 27

Other elements in 5rmf:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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 Z54226006 (pdb code 5rmf). 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 Z54226006, PDB code: 5rmf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:55.1
occ:1.00
 SG A:CYS55 2.1 56.7 1.0
SG A:CYS50 2.2 55.9 1.0
ND1 A:HIS75 2.3 53.9 1.0
SG A:CYS72 2.6 52.5 1.0
CB A:CYS50 3.1 58.9 1.0
CB A:CYS55 3.2 56.5 1.0
CE1 A:HIS75 3.2 58.3 1.0
CG A:HIS75 3.3 51.3 1.0
CB A:CYS72 3.3 55.6 1.0
CB A:HIS75 3.6 50.2 1.0
N A:CYS72 3.8 51.6 1.0
CA A:CYS72 4.1 56.5 1.0
NE2 A:HIS75 4.4 54.0 1.0
CB A:ALA52 4.4 56.4 1.0
CD2 A:HIS75 4.4 53.4 1.0
N A:HIS75 4.5 54.1 1.0
CG2 A:VAL57 4.5 53.0 1.0
CA A:CYS50 4.6 55.9 1.0
CA A:CYS55 4.6 59.7 1.0
CB A:VAL57 4.7 52.8 1.0
CA A:HIS75 4.7 49.0 1.0
C A:TYR71 4.9 45.9 1.0
C A:CYS72 4.9 60.3 1.0

Zinc binding site 2 out of 6 in 5rmf

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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 Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:51.3
occ:1.00
 NE2 A:HIS33 2.0 34.9 1.0
ND1 A:HIS39 2.1 62.1 1.0
SG A:CYS16 2.2 76.7 1.0
SG A:CYS19 2.3 50.4 1.0
CE1 A:HIS33 2.7 38.6 1.0
CG A:HIS39 3.0 68.5 1.0
CE1 A:HIS39 3.1 66.3 1.0
CD2 A:HIS33 3.2 41.9 1.0
N A:CYS19 3.2 52.7 1.0
CB A:HIS39 3.3 66.6 1.0
CB A:CYS16 3.4 66.8 1.0
CB A:CYS19 3.5 46.7 1.0
CA A:CYS19 3.7 52.9 1.0
ND1 A:HIS33 4.0 43.4 1.0
C A:ALA18 4.1 59.5 1.0
NE2 A:HIS39 4.1 64.7 1.0
CD2 A:HIS39 4.1 72.3 1.0
CB A:ALA18 4.2 67.6 1.0
CG A:HIS33 4.2 45.6 1.0
CB A:ALA110 4.5 51.0 1.0
CA A:ALA18 4.6 63.0 1.0
N A:ALA18 4.7 58.7 1.0
CA A:CYS16 4.7 65.7 1.0
CA A:HIS39 4.8 60.8 1.0
CE2 A:PHE106 4.9 54.4 1.0
CZ A:PHE106 5.0 55.4 1.0

Zinc binding site 3 out of 6 in 5rmf

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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 Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:81.2
occ:1.00
 SG A:CYS5 2.2 76.0 1.0
SG A:CYS8 2.3 0.3 1.0
SG A:CYS29 2.4 74.8 1.0
SG A:CYS26 2.6 76.5 1.0
CB A:CYS29 3.0 75.3 1.0
CB A:CYS26 3.1 71.5 1.0
CB A:CYS5 3.4 78.2 1.0
N A:CYS26 3.7 71.6 1.0
CB A:CYS8 3.8 94.2 1.0
N A:CYS8 3.9 95.0 1.0
CA A:CYS26 3.9 73.0 1.0
O A:CYS26 4.2 79.1 1.0
CA A:CYS29 4.3 70.7 1.0
CB A:LEU7 4.3 90.8 1.0
N A:CYS29 4.3 72.2 1.0
CA A:CYS8 4.3 96.5 1.0
C A:CYS26 4.5 78.3 1.0
C A:LEU7 4.7 88.9 1.0
CB A:SER10 4.7 87.5 1.0
CA A:CYS5 4.8 81.1 1.0
N A:LEU7 4.8 75.8 1.0
CA A:LEU7 4.8 85.4 1.0
C A:LEU25 4.9 72.0 1.0
OG A:SER10 4.9 77.0 1.0
C A:CYS8 5.0 93.5 1.0

Zinc binding site 4 out of 6 in 5rmf

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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 Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:42.1
occ:1.00
 NE2 B:HIS33 2.0 37.5 1.0
ND1 B:HIS39 2.2 52.6 1.0
SG B:CYS16 2.2 44.2 1.0
SG B:CYS19 2.4 43.2 1.0
CE1 B:HIS33 2.9 38.5 1.0
CD2 B:HIS33 3.0 40.0 1.0
CG B:HIS39 3.1 58.2 1.0
CE1 B:HIS39 3.1 54.0 1.0
CB B:HIS39 3.3 52.0 1.0
N B:CYS19 3.4 54.4 1.0
CB B:CYS16 3.4 54.7 1.0
CB B:CYS19 3.5 40.6 1.0
CA B:CYS19 3.9 47.8 1.0
ND1 B:HIS33 4.1 37.8 1.0
CG B:HIS33 4.1 40.9 1.0
CD2 B:HIS39 4.2 55.1 1.0
NE2 B:HIS39 4.2 55.5 1.0
C B:ALA18 4.3 55.0 1.0
CB B:ALA18 4.4 46.8 1.0
CB B:ALA110 4.4 41.1 1.0
CA B:ALA18 4.7 50.4 1.0
CA B:CYS16 4.8 56.3 1.0
CA B:HIS39 4.8 51.2 1.0
N B:ALA18 4.8 50.1 1.0
CE2 B:PHE106 4.9 44.4 1.0
CZ B:PHE106 5.0 45.8 1.0

Zinc binding site 5 out of 6 in 5rmf

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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 Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:75.2
occ:1.00
 SG B:CYS5 2.0 85.6 1.0
SG B:CYS26 2.1 71.1 1.0
SG B:CYS29 2.6 61.5 1.0
CB B:CYS29 2.9 68.3 1.0
CB B:CYS26 3.0 66.5 1.0
CB B:CYS5 3.2 87.1 1.0
SG B:CYS8 3.3 91.7 1.0
N B:CYS26 3.5 82.5 1.0
CB B:CYS8 3.7 91.4 1.0
N B:CYS8 3.8 92.6 1.0
CA B:CYS26 3.8 77.9 1.0
CA B:CYS29 4.2 69.4 1.0
O B:CYS26 4.3 78.3 1.0
CA B:CYS8 4.3 89.8 1.0
N B:CYS29 4.3 74.5 1.0
CB B:LEU7 4.3 94.0 1.0
C B:CYS26 4.5 84.0 1.0
C B:LEU7 4.5 90.2 1.0
CA B:CYS5 4.6 84.9 1.0
OG B:SER10 4.6 63.3 1.0
N B:LEU7 4.6 77.2 1.0
CB B:SER10 4.7 65.5 1.0
C B:LEU25 4.7 79.8 1.0
CA B:LEU7 4.7 90.0 1.0
N B:GLY99 4.9 87.8 1.0
N B:ASN9 5.0 78.0 1.0
CA B:GLY99 5.0 81.1 1.0
CA B:LEU25 5.0 72.0 1.0

Zinc binding site 6 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.9
occ:1.00
 SG B:CYS50 2.2 68.0 1.0
SG B:CYS55 2.2 88.1 1.0
ND1 B:HIS75 2.5 83.5 1.0
SG B:CYS72 2.7 63.8 1.0
CB B:CYS50 3.2 74.8 1.0
CB B:CYS55 3.3 93.3 1.0
CG B:HIS75 3.3 85.1 1.0
CB B:CYS72 3.4 68.0 1.0
CB B:HIS75 3.4 85.2 1.0
CE1 B:HIS75 3.6 85.8 1.0
N B:CYS72 3.7 67.3 1.0
CA B:CYS72 4.1 68.2 1.0
N B:HIS75 4.3 73.3 1.0
CB B:ALA52 4.3 86.2 1.0
CG2 B:VAL57 4.4 0.2 1.0
CA B:HIS75 4.5 82.9 1.0
CD2 B:HIS75 4.5 86.1 1.0
CA B:CYS50 4.6 75.9 1.0
NE2 B:HIS75 4.6 87.2 1.0
CB B:VAL57 4.6 0.1 1.0
CA B:CYS55 4.7 93.8 1.0
C B:CYS72 4.9 71.9 1.0
C B:TYR71 4.9 74.0 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: Wed Dec 16 08:18:29 2020

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