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Zinc in PDB 5rml: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z85956652

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z85956652

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z85956652:
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 Z85956652, PDB code: 5rml 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) 81.52 / 2.43
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.940, 70.101, 85.447, 102.81, 95.84, 112.42
R / Rfree (%) 20.7 / 28.9

Other elements in 5rml:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z85956652 also contains other interesting chemical elements:

Chlorine (Cl) 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 Z85956652 (pdb code 5rml). 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 Z85956652, PDB code: 5rml:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rml

Go back to Zinc Binding Sites List in 5rml
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z85956652


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 Z85956652 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:44.3
occ:1.00
 SG B:CYS16 2.1 50.5 1.0
NE2 B:HIS33 2.1 36.0 1.0
ND1 B:HIS39 2.2 63.7 1.0
SG B:CYS19 2.5 43.5 1.0
CB B:CYS16 3.0 48.0 1.0
CG B:HIS39 3.1 63.5 1.0
CD2 B:HIS33 3.1 34.8 1.0
CE1 B:HIS33 3.1 41.6 1.0
CB B:HIS39 3.2 61.8 1.0
CE1 B:HIS39 3.3 61.5 1.0
CB B:CYS19 3.3 49.5 1.0
N B:CYS19 3.4 60.6 1.0
CA B:CYS19 3.7 54.9 1.0
ND1 B:HIS33 4.2 44.1 1.0
CG B:HIS33 4.2 39.0 1.0
CD2 B:HIS39 4.2 64.1 1.0
NE2 B:HIS39 4.3 60.8 1.0
C B:ALA18 4.3 63.1 1.0
CA B:CYS16 4.4 51.2 1.0
CB B:ALA110 4.6 42.6 1.0
CA B:HIS39 4.7 58.2 1.0
CB B:ALA18 4.7 49.8 1.0
C B:CYS16 4.7 49.9 1.0
N B:ALA18 4.8 53.8 1.0
CA B:ALA18 4.9 55.6 1.0
O B:CYS16 4.9 55.1 1.0

Zinc binding site 2 out of 6 in 5rml

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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 Z85956652


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 Z85956652 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:57.0
occ:1.00
 SG B:CYS5 1.7 73.0 1.0
SG B:CYS26 2.1 77.5 1.0
SG B:CYS29 2.6 56.0 1.0
CB B:CYS8 2.8 82.7 1.0
CB B:CYS5 2.8 79.9 1.0
CB B:CYS26 3.0 62.9 1.0
CB B:CYS29 3.1 54.4 1.0
SG B:CYS8 3.2 95.1 1.0
N B:CYS8 3.6 88.7 1.0
N B:CYS26 3.7 78.8 1.0
CA B:CYS8 3.8 86.0 1.0
CA B:CYS26 3.9 75.0 1.0
N B:CYS29 4.2 59.1 1.0
CB B:SER10 4.2 64.0 1.0
CA B:CYS5 4.2 81.8 1.0
CA B:CYS29 4.2 56.2 1.0
O B:CYS26 4.4 89.7 1.0
C B:CYS26 4.6 78.6 1.0
C B:LEU7 4.6 90.4 1.0
CB B:LEU7 4.7 0.6 1.0
OG B:SER10 4.7 70.2 1.0
C B:CYS8 4.8 78.2 1.0
C B:CYS5 4.8 84.9 1.0
C B:LEU25 4.8 62.7 1.0
N B:LEU7 4.9 73.1 1.0
N B:ASN9 4.9 74.7 1.0
N B:GLY99 4.9 77.0 1.0
CA B:LEU7 5.0 92.2 1.0

Zinc binding site 3 out of 6 in 5rml

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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 Z85956652


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 Z85956652 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:92.3
occ:1.00
 ND1 B:HIS75 2.4 1.0 1.0
SG B:CYS55 2.4 0.0 1.0
SG B:CYS50 2.5 0.2 1.0
SG B:CYS72 2.7 0.0 1.0
CB B:CYS55 2.8 0.6 1.0
CE1 B:HIS75 3.2 0.1 1.0
CB B:CYS50 3.3 0.4 1.0
CG B:HIS75 3.4 1.0 1.0
CB B:CYS72 3.5 77.1 1.0
CB B:HIS75 3.8 0.6 1.0
CB B:ALA52 4.0 0.2 1.0
N B:CYS72 4.0 69.9 1.0
CG2 B:VAL57 4.1 1.0 1.0
NE2 B:HIS75 4.2 0.9 1.0
CA B:CYS55 4.3 0.6 1.0
CD2 B:HIS75 4.3 0.7 1.0
CA B:CYS72 4.3 79.4 1.0
CB B:VAL57 4.4 0.5 1.0
N B:HIS75 4.6 83.8 1.0
C B:CYS55 4.7 1.0 1.0
CA B:CYS50 4.8 0.5 1.0
CA B:HIS75 4.9 92.6 1.0
O B:CYS55 4.9 0.7 1.0

Zinc binding site 4 out of 6 in 5rml

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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 Z85956652


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 Z85956652 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:68.4
occ:1.00
 SG A:CYS55 2.0 68.3 1.0
ND1 A:HIS75 2.2 52.5 1.0
SG A:CYS50 2.3 62.3 1.0
SG A:CYS72 2.3 58.8 1.0
CB A:CYS55 3.0 61.6 1.0
CE1 A:HIS75 3.0 55.0 1.0
CB A:CYS50 3.3 64.9 1.0
CG A:HIS75 3.4 47.2 1.0
CB A:CYS72 3.5 64.2 1.0
CB A:HIS75 3.8 48.9 1.0
N A:CYS72 4.0 60.7 1.0
CB A:ALA52 4.2 71.1 1.0
NE2 A:HIS75 4.2 47.6 1.0
CA A:CYS72 4.3 64.8 1.0
CD2 A:HIS75 4.4 48.7 1.0
CA A:CYS55 4.4 68.8 1.0
CA A:CYS50 4.7 67.1 1.0
N A:HIS75 4.8 56.2 1.0
CB A:VAL57 4.9 75.7 1.0
CG2 A:VAL57 4.9 81.5 1.0
CA A:HIS75 4.9 52.6 1.0

Zinc binding site 5 out of 6 in 5rml

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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 Z85956652


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 Z85956652 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:65.4
occ:1.00
 NE2 A:HIS33 1.8 40.3 1.0
ND1 A:HIS39 2.1 81.3 1.0
SG A:CYS16 2.2 97.2 1.0
SG A:CYS19 2.4 60.5 1.0
CE1 A:HIS33 2.7 44.8 1.0
CD2 A:HIS33 2.8 46.8 1.0
N A:CYS19 2.9 52.5 1.0
CE1 A:HIS39 3.0 82.2 1.0
CG A:HIS39 3.1 86.5 1.0
CB A:CYS16 3.4 89.5 1.0
CB A:CYS19 3.4 48.4 1.0
CB A:HIS39 3.4 82.5 1.0
CA A:CYS19 3.5 54.5 1.0
C A:ALA18 3.6 61.5 1.0
ND1 A:HIS33 3.8 52.0 1.0
CG A:HIS33 3.9 51.7 1.0
NE2 A:HIS39 4.2 79.9 1.0
CB A:ALA18 4.2 75.3 1.0
CD2 A:HIS39 4.2 89.2 1.0
O A:ALA18 4.2 68.7 1.0
CA A:ALA18 4.3 70.0 1.0
N A:ALA18 4.5 72.3 1.0
CB A:ALA110 4.6 62.7 1.0
CA A:CYS16 4.7 86.0 1.0
CE2 A:PHE106 4.8 68.8 1.0
C A:CYS16 4.9 68.6 1.0
O A:CYS16 4.9 74.7 1.0
CA A:HIS39 4.9 74.0 1.0

Zinc binding site 6 out of 6 in 5rml

Go back to Zinc Binding Sites List in 5rml
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z85956652


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 Z85956652 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:87.2
occ:1.00
 SG A:CYS5 2.3 0.5 1.0
SG A:CYS29 2.6 76.5 1.0
SG A:CYS26 2.6 0.8 1.0
SG A:CYS8 2.7 0.5 1.0
CB A:CYS26 2.9 99.8 1.0
CB A:CYS29 3.1 88.2 1.0
N A:CYS26 3.6 93.8 1.0
CB A:CYS5 3.6 97.6 1.0
CB A:CYS8 3.7 0.9 1.0
CA A:CYS26 3.8 96.6 1.0
N A:CYS8 3.9 0.1 1.0
O A:CYS26 4.3 90.1 1.0
CB A:LEU7 4.3 0.5 1.0
CA A:CYS29 4.4 89.5 1.0
CA A:CYS8 4.4 0.5 1.0
C A:CYS26 4.4 96.3 1.0
N A:CYS29 4.4 98.9 1.0
C A:LEU7 4.7 0.9 1.0
C A:LEU25 4.8 93.8 1.0
CA A:LEU7 4.9 0.1 1.0
CA A:CYS5 4.9 0.9 1.0
N A:LEU7 4.9 92.4 1.0
O A:CYS5 4.9 89.4 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 04:29:04 2024

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