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Zinc in PDB 5rm2: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1741964527

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1741964527

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1741964527:
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 Z1741964527, PDB code: 5rm2 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 / 1.82
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.992, 70.150, 85.128, 102.34, 96.21, 112.56
R / Rfree (%) 23.1 / 27.3

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 Z1741964527 (pdb code 5rm2). 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 Z1741964527, PDB code: 5rm2:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm2

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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 Z1741964527


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 Z1741964527 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:57.2
occ:1.00
 SG A:CYS50 2.2 59.2 1.0
SG A:CYS55 2.2 56.1 1.0
ND1 A:HIS75 2.4 45.9 1.0
SG A:CYS72 2.5 53.8 1.0
CB A:CYS50 3.1 64.7 1.0
CB A:CYS72 3.3 55.9 1.0
CG A:HIS75 3.3 47.5 1.0
CB A:CYS55 3.3 60.4 1.0
CE1 A:HIS75 3.4 52.6 1.0
CB A:HIS75 3.5 50.3 1.0
N A:CYS72 3.7 47.3 1.0
CA A:CYS72 4.1 53.0 1.0
CB A:ALA52 4.4 49.5 1.0
CD2 A:HIS75 4.4 48.3 1.0
NE2 A:HIS75 4.5 50.8 1.0
CG2 A:VAL57 4.5 59.3 1.0
CA A:CYS50 4.5 62.0 1.0
N A:HIS75 4.5 59.1 1.0
CA A:HIS75 4.6 52.2 1.0
CB A:VAL57 4.7 59.3 1.0
CA A:CYS55 4.7 61.9 1.0
C A:CYS72 4.8 59.1 1.0
C A:TYR71 4.8 47.9 1.0

Zinc binding site 2 out of 6 in 5rm2

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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 Z1741964527


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 Z1741964527 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:51.6
occ:1.00
 NE2 A:HIS33 1.9 23.4 1.0
ND1 A:HIS39 2.1 59.6 1.0
SG A:CYS16 2.3 66.2 1.0
SG A:CYS19 2.5 51.7 1.0
CE1 A:HIS33 2.8 31.6 1.0
CD2 A:HIS33 3.0 33.7 1.0
CE1 A:HIS39 3.0 59.5 1.0
CG A:HIS39 3.1 61.9 1.0
N A:CYS19 3.2 57.7 1.0
CB A:CYS16 3.3 67.6 1.0
CB A:HIS39 3.4 56.0 1.0
CB A:CYS19 3.4 43.7 1.0
CA A:CYS19 3.7 54.7 1.0
ND1 A:HIS33 4.0 32.5 1.0
CG A:HIS33 4.1 34.6 1.0
NE2 A:HIS39 4.2 60.5 1.0
CD2 A:HIS39 4.2 59.8 1.0
C A:ALA18 4.2 59.7 1.0
CB A:ALA18 4.4 60.8 1.0
CB A:ALA110 4.5 53.4 1.0
CA A:CYS16 4.7 63.8 1.0
CA A:ALA18 4.7 61.1 1.0
N A:ALA18 4.8 57.5 1.0
CA A:HIS39 4.9 54.0 1.0
O A:CYS16 4.9 60.1 1.0
CE2 A:PHE106 4.9 47.0 1.0
C A:CYS16 4.9 59.5 1.0
CZ A:PHE106 5.0 51.3 1.0

Zinc binding site 3 out of 6 in 5rm2

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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 Z1741964527


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 Z1741964527 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:86.1
occ:1.00
 SG A:CYS8 2.1 95.6 1.0
SG A:CYS5 2.2 65.5 1.0
SG A:CYS29 2.4 84.9 1.0
SG A:CYS26 2.7 77.8 1.0
CB A:CYS29 3.1 89.3 1.0
CB A:CYS26 3.3 73.4 1.0
CB A:CYS5 3.3 74.2 1.0
CB A:CYS8 3.5 93.7 1.0
N A:CYS8 3.6 94.4 1.0
N A:CYS26 3.9 68.4 1.0
CA A:CYS8 4.0 92.1 1.0
CA A:CYS26 4.1 73.2 1.0
CB A:LEU7 4.2 87.1 1.0
CA A:CYS29 4.4 84.2 1.0
N A:CYS29 4.4 86.2 1.0
C A:LEU7 4.5 89.4 1.0
C A:CYS8 4.5 89.0 1.0
N A:ASN9 4.6 91.5 1.0
CA A:CYS5 4.6 74.8 1.0
CA A:LEU7 4.7 83.9 1.0
N A:LEU7 4.7 72.0 1.0
C A:CYS26 4.9 81.3 1.0
CB A:SER10 4.9 82.1 1.0
O A:CYS26 5.0 82.7 1.0
C A:CYS5 5.0 75.9 1.0

Zinc binding site 4 out of 6 in 5rm2

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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 Z1741964527


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 Z1741964527 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:38.4
occ:1.00
 NE2 B:HIS33 2.0 29.8 1.0
ND1 B:HIS39 2.2 43.2 1.0
SG B:CYS16 2.3 42.1 1.0
SG B:CYS19 2.4 41.3 1.0
CD2 B:HIS33 2.9 27.7 1.0
CE1 B:HIS33 3.0 32.5 1.0
CG B:HIS39 3.1 47.6 1.0
CE1 B:HIS39 3.2 48.4 1.0
CB B:CYS16 3.3 44.7 1.0
CB B:HIS39 3.3 44.9 1.0
CB B:CYS19 3.4 38.5 1.0
N B:CYS19 3.5 46.7 1.0
CA B:CYS19 3.8 43.1 1.0
ND1 B:HIS33 4.1 30.1 1.0
CG B:HIS33 4.1 28.8 1.0
CD2 B:HIS39 4.3 46.5 1.0
NE2 B:HIS39 4.3 47.3 1.0
C B:ALA18 4.4 46.6 1.0
CB B:ALA110 4.5 43.5 1.0
CB B:ALA18 4.5 40.5 1.0
CA B:CYS16 4.7 44.5 1.0
CA B:HIS39 4.8 46.7 1.0
CA B:ALA18 4.9 44.0 1.0
N B:ALA18 4.9 41.1 1.0
CE2 B:PHE106 4.9 30.4 1.0
C B:CYS16 5.0 44.3 1.0

Zinc binding site 5 out of 6 in 5rm2

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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 Z1741964527


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 Z1741964527 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:56.4
occ:1.00
 SG B:CYS5 2.3 50.8 1.0
SG B:CYS29 2.4 42.3 1.0
SG B:CYS26 2.5 56.9 1.0
CB B:CYS8 2.7 64.1 1.0
CB B:CYS26 3.1 49.1 1.0
CB B:CYS29 3.2 42.5 1.0
SG B:CYS8 3.2 73.0 1.0
CB B:CYS5 3.3 61.1 1.0
N B:CYS26 3.7 53.8 1.0
N B:CYS8 3.7 71.3 1.0
CA B:CYS8 3.8 67.7 1.0
CA B:CYS26 4.0 58.6 1.0
N B:CYS29 4.2 42.6 1.0
CA B:CYS29 4.3 43.0 1.0
CB B:LEU7 4.6 71.3 1.0
C B:LEU7 4.6 69.4 1.0
CB B:SER10 4.6 67.8 1.0
CA B:CYS5 4.7 65.1 1.0
OG B:SER10 4.8 67.5 1.0
C B:CYS26 4.8 60.0 1.0
C B:CYS8 4.8 62.5 1.0
N B:GLY99 4.9 65.4 1.0
C B:LEU25 4.9 53.8 1.0
N B:ASN9 4.9 67.0 1.0
CA B:GLY99 4.9 61.7 1.0
N B:LEU7 4.9 56.9 1.0
CA B:LEU7 5.0 65.5 1.0
O B:CYS26 5.0 53.5 1.0

Zinc binding site 6 out of 6 in 5rm2

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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 Z1741964527


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 Z1741964527 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:71.5
occ:1.00
 SG B:CYS55 2.2 77.5 1.0
SG B:CYS50 2.3 63.7 1.0
SG B:CYS72 2.5 59.6 1.0
ND1 B:HIS75 2.6 83.8 1.0
CB B:CYS50 3.0 68.9 1.0
CB B:CYS55 3.2 82.2 1.0
CB B:CYS72 3.3 59.6 1.0
CG B:HIS75 3.4 80.0 1.0
CB B:HIS75 3.6 70.3 1.0
CE1 B:HIS75 3.6 83.2 1.0
N B:CYS72 3.7 57.2 1.0
CA B:CYS72 4.1 62.0 1.0
CG2 B:VAL57 4.4 76.5 1.0
CB B:ALA52 4.4 93.2 1.0
CA B:CYS50 4.5 71.3 1.0
N B:HIS75 4.6 55.5 1.0
CA B:CYS55 4.6 85.9 1.0
CD2 B:HIS75 4.6 82.5 1.0
CB B:VAL57 4.6 78.7 1.0
NE2 B:HIS75 4.7 84.7 1.0
CA B:HIS75 4.7 64.6 1.0
C B:TYR71 4.8 57.8 1.0
C B:CYS72 4.9 70.5 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 04:11:57 2024

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