Atomistry » Zinc » PDB 5rlf-5rmj » 5rli
Atomistry »
  Zinc »
    PDB 5rlf-5rmj »
      5rli »

Zinc in PDB 5rli: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795:
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 Z45617795, PDB code: 5rli 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) 81.01 / 2.26
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.846, 70.009, 84.938, 102.88, 95.84, 112.37
R / Rfree (%) 19.7 / 26.8

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 Z45617795 (pdb code 5rli). 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 Z45617795, PDB code: 5rli:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rli

Go back to Zinc Binding Sites List in 5rli
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:54.5
occ:1.00
 SG A:CYS55 2.2 54.9 1.0
SG A:CYS50 2.3 51.8 1.0
ND1 A:HIS75 2.3 41.5 1.0
SG A:CYS72 2.5 56.6 1.0
CB A:CYS50 3.2 57.1 1.0
CE1 A:HIS75 3.3 46.8 1.0
CB A:CYS55 3.3 54.4 1.0
CG A:HIS75 3.3 39.7 1.0
CB A:CYS72 3.4 58.9 1.0
CB A:HIS75 3.5 43.6 1.0
N A:CYS72 3.8 51.0 1.0
CA A:CYS72 4.2 59.0 1.0
CB A:ALA52 4.2 55.5 1.0
NE2 A:HIS75 4.4 43.3 1.0
CD2 A:HIS75 4.4 39.9 1.0
CG2 A:VAL57 4.6 55.9 1.0
CA A:CYS50 4.7 52.5 1.0
CA A:CYS55 4.7 58.3 1.0
N A:HIS75 4.7 51.5 1.0
CB A:VAL57 4.7 55.8 1.0
CA A:HIS75 4.7 43.5 1.0
C A:TYR71 4.9 45.1 1.0
C A:CYS72 4.9 64.0 1.0

Zinc binding site 2 out of 6 in 5rli

Go back to Zinc Binding Sites List in 5rli
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:48.3
occ:1.00
 NE2 A:HIS33 1.8 30.8 1.0
ND1 A:HIS39 2.1 67.0 1.0
SG A:CYS16 2.3 74.0 1.0
SG A:CYS19 2.5 48.1 1.0
CE1 A:HIS33 2.7 34.5 1.0
CD2 A:HIS33 2.9 38.0 1.0
N A:CYS19 3.1 42.4 1.0
CE1 A:HIS39 3.1 72.9 1.0
CG A:HIS39 3.1 67.6 1.0
CB A:CYS16 3.3 67.9 1.0
CB A:HIS39 3.4 61.5 1.0
CB A:CYS19 3.4 40.1 1.0
CA A:CYS19 3.6 45.1 1.0
ND1 A:HIS33 3.9 38.9 1.0
CG A:HIS33 4.0 41.1 1.0
C A:ALA18 4.1 58.8 1.0
CB A:ALA18 4.2 63.6 1.0
NE2 A:HIS39 4.2 67.9 1.0
CD2 A:HIS39 4.2 74.0 1.0
CB A:ALA110 4.4 57.7 1.0
CA A:ALA18 4.5 64.5 1.0
CA A:CYS16 4.7 64.3 1.0
N A:ALA18 4.7 59.0 1.0
CA A:HIS39 4.8 57.2 1.0
CE2 A:PHE106 4.9 43.7 1.0

Zinc binding site 3 out of 6 in 5rli

Go back to Zinc Binding Sites List in 5rli
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:83.6
occ:1.00
 SG A:CYS5 2.0 69.8 1.0
SG A:CYS8 2.4 88.4 1.0
SG A:CYS29 2.4 69.0 1.0
SG A:CYS26 2.7 63.7 1.0
CB A:CYS29 3.0 76.7 1.0
CB A:CYS26 3.1 65.0 1.0
CB A:CYS5 3.2 77.5 1.0
CB A:CYS8 3.6 88.0 1.0
N A:CYS26 3.7 66.8 1.0
N A:CYS8 3.9 86.2 1.0
CA A:CYS26 4.0 67.8 1.0
CA A:CYS8 4.2 86.1 1.0
CA A:CYS29 4.3 75.2 1.0
CB A:LEU7 4.4 75.5 1.0
N A:CYS29 4.4 76.1 1.0
O A:CYS26 4.6 80.0 1.0
CA A:CYS5 4.6 84.8 1.0
C A:CYS26 4.7 76.7 1.0
C A:CYS8 4.8 84.1 1.0
N A:ASN9 4.8 87.2 1.0
C A:LEU7 4.8 82.1 1.0
C A:CYS5 4.9 89.3 1.0
N A:LEU7 4.9 71.9 1.0
CB A:SER10 4.9 71.4 1.0
C A:LEU25 4.9 68.6 1.0
O A:CYS5 4.9 81.3 1.0
CA A:LEU7 5.0 78.8 1.0

Zinc binding site 4 out of 6 in 5rli

Go back to Zinc Binding Sites List in 5rli
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:36.9
occ:1.00
 NE2 B:HIS33 1.9 29.9 1.0
ND1 B:HIS39 2.1 46.3 1.0
SG B:CYS16 2.2 41.3 1.0
SG B:CYS19 2.3 37.3 1.0
CD2 B:HIS33 2.9 33.3 1.0
CE1 B:HIS33 2.9 30.6 1.0
CG B:HIS39 3.1 48.7 1.0
CE1 B:HIS39 3.1 47.0 1.0
CB B:HIS39 3.3 46.2 1.0
CB B:CYS19 3.3 35.1 1.0
CB B:CYS16 3.3 40.4 1.0
N B:CYS19 3.3 45.9 1.0
CA B:CYS19 3.7 42.4 1.0
ND1 B:HIS33 4.0 30.0 1.0
CG B:HIS33 4.0 32.4 1.0
C B:ALA18 4.2 46.5 1.0
CD2 B:HIS39 4.2 45.7 1.0
NE2 B:HIS39 4.2 49.4 1.0
CB B:ALA110 4.5 35.0 1.0
CB B:ALA18 4.6 40.7 1.0
CA B:CYS16 4.7 39.2 1.0
CA B:ALA18 4.8 44.7 1.0
CA B:HIS39 4.8 42.9 1.0
N B:ALA18 4.9 44.7 1.0
O B:ALA18 4.9 43.8 1.0

Zinc binding site 5 out of 6 in 5rli

Go back to Zinc Binding Sites List in 5rli
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:49.4
occ:1.00
 SG B:CYS29 2.2 47.4 1.0
SG B:CYS26 2.3 50.6 1.0
SG B:CYS5 2.4 53.7 1.0
CB B:CYS8 2.8 69.0 1.0
CB B:CYS29 3.0 47.4 1.0
SG B:CYS8 3.2 88.0 1.0
CB B:CYS5 3.4 60.3 1.0
CB B:CYS26 3.5 52.0 1.0
N B:CYS8 3.7 71.2 1.0
CA B:CYS8 3.8 74.1 1.0
N B:CYS26 4.0 55.1 1.0
N B:CYS29 4.0 50.2 1.0
CA B:CYS29 4.1 44.9 1.0
CA B:CYS26 4.3 52.9 1.0
CB B:LEU7 4.4 71.9 1.0
OG B:SER10 4.5 63.5 1.0
CB B:SER10 4.5 63.1 1.0
CA B:GLY99 4.6 62.7 1.0
N B:GLY99 4.6 63.5 1.0
C B:LEU7 4.6 72.7 1.0
CA B:CYS5 4.9 61.6 1.0
C B:CYS8 4.9 67.5 1.0
C B:CYS26 4.9 54.6 1.0
CA B:LEU7 5.0 70.2 1.0

Zinc binding site 6 out of 6 in 5rli

Go back to Zinc Binding Sites List in 5rli
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z45617795


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 Z45617795 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn705

b:62.1
occ:1.00
 SG B:CYS50 2.2 60.4 1.0
SG B:CYS55 2.3 65.5 1.0
ND1 B:HIS75 2.4 73.8 1.0
SG B:CYS72 2.6 54.2 1.0
CB B:CYS50 3.1 62.0 1.0
CB B:CYS55 3.2 74.1 1.0
CG B:HIS75 3.3 74.2 1.0
CB B:HIS75 3.4 65.1 1.0
CE1 B:HIS75 3.4 73.5 1.0
CB B:CYS72 3.5 59.5 1.0
N B:CYS72 3.8 52.7 1.0
CB B:ALA52 4.1 77.0 1.0
CA B:CYS72 4.2 60.2 1.0
CG2 B:VAL57 4.3 78.1 1.0
CD2 B:HIS75 4.5 78.1 1.0
N B:HIS75 4.5 56.2 1.0
NE2 B:HIS75 4.5 76.0 1.0
CA B:CYS50 4.5 63.2 1.0
CA B:HIS75 4.6 61.5 1.0
CA B:CYS55 4.6 78.1 1.0
CB B:VAL57 4.7 78.3 1.0
C B:CYS72 4.9 64.7 1.0
C B:TYR71 4.9 54.6 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 04:00:42 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy