Atomistry » Zinc » PDB 5rli-5rmm » 5rm0
Atomistry »
  Zinc »
    PDB 5rli-5rmm »
      5rm0 »

Zinc in PDB 5rm0: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719:
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 Z1492796719, PDB code: 5rm0 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) 81.27 / 1.91
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.095, 70.190, 85.226, 102.66, 96.15, 112.43
R / Rfree (%) 16.8 / 23.9

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 Z1492796719 (pdb code 5rm0). 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 Z1492796719, PDB code: 5rm0:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm0

Go back to Zinc Binding Sites List in 5rm0
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:72.2
occ:1.00
 SG A:CYS50 2.3 70.9 1.0
ND1 A:HIS75 2.3 65.3 1.0
SG A:CYS55 2.3 81.7 1.0
SG A:CYS72 2.8 70.0 1.0
CB A:CYS50 3.2 74.4 1.0
CB A:CYS55 3.3 81.5 1.0
CE1 A:HIS75 3.3 65.7 1.0
CG A:HIS75 3.3 64.7 1.0
CB A:CYS72 3.4 73.6 1.0
CB A:HIS75 3.6 64.5 1.0
N A:CYS72 3.8 68.6 1.0
CA A:CYS72 4.2 71.9 1.0
CB A:ALA52 4.3 69.7 1.0
NE2 A:HIS75 4.4 63.4 1.0
CG2 A:VAL57 4.4 75.7 1.0
CD2 A:HIS75 4.5 64.0 1.0
N A:HIS75 4.5 69.5 1.0
CA A:CYS50 4.6 72.8 1.0
CB A:VAL57 4.6 75.1 1.0
CA A:CYS55 4.7 84.4 1.0
CA A:HIS75 4.7 66.9 1.0
C A:TYR71 4.9 64.1 1.0
C A:CYS72 5.0 76.0 1.0

Zinc binding site 2 out of 6 in 5rm0

Go back to Zinc Binding Sites List in 5rm0
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:69.4
occ:1.00
 ND1 A:HIS39 2.0 76.4 1.0
NE2 A:HIS33 2.0 59.7 1.0
SG A:CYS16 2.4 79.6 1.0
SG A:CYS19 2.5 68.5 1.0
CE1 A:HIS33 3.0 60.8 1.0
CE1 A:HIS39 3.0 77.1 1.0
CG A:HIS39 3.0 77.9 1.0
CD2 A:HIS33 3.0 62.9 1.0
CB A:HIS39 3.3 73.2 1.0
CB A:CYS19 3.4 67.1 1.0
N A:CYS19 3.4 71.0 1.0
CB A:CYS16 3.5 78.0 1.0
CA A:CYS19 3.8 70.1 1.0
C A:ALA18 4.1 77.7 1.0
ND1 A:HIS33 4.1 63.3 1.0
NE2 A:HIS39 4.2 78.3 1.0
CG A:HIS33 4.2 66.1 1.0
CD2 A:HIS39 4.2 78.6 1.0
CB A:ALA18 4.4 77.2 1.0
CB A:ALA110 4.4 63.0 1.0
CA A:ALA18 4.6 77.2 1.0
N A:ALA18 4.8 75.5 1.0
O A:ALA18 4.8 80.1 1.0
CA A:CYS16 4.8 78.3 1.0
CA A:HIS39 4.8 74.0 1.0
CE2 A:PHE106 5.0 75.7 1.0

Zinc binding site 3 out of 6 in 5rm0

Go back to Zinc Binding Sites List in 5rm0
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.2
occ:1.00
 SG A:CYS26 2.2 92.4 1.0
SG A:CYS5 2.3 93.5 1.0
SG A:CYS8 2.4 0.7 1.0
SG A:CYS29 2.5 100.0 1.0
CB A:CYS29 3.3 96.0 1.0
CB A:CYS5 3.4 91.1 1.0
CB A:CYS8 3.4 0.5 1.0
CB A:CYS26 3.5 93.5 1.0
N A:CYS8 3.6 0.9 1.0
CA A:CYS8 4.0 0.3 1.0
N A:CYS26 4.0 93.3 1.0
N A:CYS29 4.3 95.3 1.0
CA A:CYS26 4.3 97.2 1.0
CB A:LEU7 4.3 0.6 1.0
CA A:CYS29 4.4 90.7 1.0
C A:LEU7 4.5 0.5 1.0
C A:CYS8 4.6 0.1 1.0
CA A:LEU7 4.8 0.9 1.0
CB A:SER10 4.8 0.0 1.0
N A:LEU7 4.8 0.1 1.0
CA A:CYS5 4.8 92.3 1.0
N A:ASN9 4.8 0.7 1.0
OG A:SER10 4.8 0.4 1.0
O A:CYS26 4.9 0.4 1.0
C A:CYS26 5.0 0.1 1.0

Zinc binding site 4 out of 6 in 5rm0

Go back to Zinc Binding Sites List in 5rm0
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:52.4
occ:1.00
 NE2 B:HIS33 2.1 51.9 1.0
ND1 B:HIS39 2.2 54.5 1.0
SG B:CYS16 2.2 58.1 1.0
SG B:CYS19 2.6 57.0 1.0
CD2 B:HIS33 3.0 50.6 1.0
CG B:HIS39 3.1 54.9 1.0
CE1 B:HIS33 3.1 52.0 1.0
CE1 B:HIS39 3.2 55.6 1.0
CB B:CYS16 3.3 61.8 1.0
CB B:HIS39 3.3 53.9 1.0
CB B:CYS19 3.4 55.4 1.0
N B:CYS19 3.4 57.3 1.0
CA B:CYS19 3.8 56.5 1.0
C B:ALA18 4.1 56.0 1.0
CG B:HIS33 4.2 52.0 1.0
ND1 B:HIS33 4.2 51.3 1.0
CD2 B:HIS39 4.3 56.1 1.0
NE2 B:HIS39 4.3 57.1 1.0
CB B:ALA18 4.3 52.9 1.0
CA B:ALA18 4.6 55.0 1.0
CA B:CYS16 4.6 62.4 1.0
N B:ALA18 4.7 56.8 1.0
CB B:ALA110 4.7 50.8 1.0
CA B:HIS39 4.8 54.1 1.0
O B:ALA18 4.9 54.9 1.0
C B:CYS16 4.9 64.3 1.0

Zinc binding site 5 out of 6 in 5rm0

Go back to Zinc Binding Sites List in 5rm0
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:88.7
occ:1.00
 SG B:CYS26 2.2 80.8 1.0
SG B:CYS5 2.3 74.3 1.0
SG B:CYS29 2.4 83.4 1.0
CB B:CYS8 2.8 90.0 1.0
CB B:CYS29 3.1 70.8 1.0
SG B:CYS8 3.2 96.1 1.0
CB B:CYS5 3.4 81.9 1.0
CB B:CYS26 3.5 81.5 1.0
N B:CYS8 3.7 89.7 1.0
CA B:CYS8 3.9 90.3 1.0
N B:CYS26 3.9 76.3 1.0
N B:CYS29 4.1 70.3 1.0
CA B:CYS29 4.2 67.5 1.0
CA B:CYS26 4.2 80.5 1.0
CB B:LEU7 4.4 85.8 1.0
C B:LEU7 4.6 86.4 1.0
N B:GLY99 4.8 79.7 1.0
CB B:SER10 4.8 82.3 1.0
O B:CYS26 4.8 82.4 1.0
OG B:SER10 4.8 79.1 1.0
CA B:CYS5 4.8 79.9 1.0
C B:CYS26 4.8 81.5 1.0
C B:CYS8 4.9 90.5 1.0
CA B:LEU7 4.9 85.4 1.0
N B:LEU7 4.9 82.8 1.0
CA B:GLY99 4.9 78.5 1.0

Zinc binding site 6 out of 6 in 5rm0

Go back to Zinc Binding Sites List in 5rm0
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1492796719


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 Z1492796719 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:86.5
occ:1.00
 SG B:CYS50 2.2 87.0 1.0
SG B:CYS55 2.3 0.1 1.0
ND1 B:HIS75 2.4 88.3 1.0
SG B:CYS72 2.9 84.9 1.0
CB B:CYS50 3.1 88.8 1.0
CB B:CYS55 3.2 0.7 1.0
CE1 B:HIS75 3.3 90.9 1.0
CG B:HIS75 3.4 87.6 1.0
CB B:CYS72 3.5 79.8 1.0
CB B:HIS75 3.6 85.1 1.0
N B:CYS72 3.8 80.1 1.0
CB B:ALA52 4.2 1.0 1.0
CA B:CYS72 4.3 80.3 1.0
CG2 B:VAL57 4.4 91.2 1.0
NE2 B:HIS75 4.5 92.3 1.0
CD2 B:HIS75 4.5 90.2 1.0
CA B:CYS50 4.5 90.0 1.0
N B:HIS75 4.6 85.0 1.0
CB B:VAL57 4.6 91.7 1.0
CA B:CYS55 4.6 0.1 1.0
CA B:HIS75 4.8 86.2 1.0
C B:TYR71 4.9 78.0 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: Thu Aug 21 07:21:00 2025

Last articles

Zn in 6A9O
Zn in 6AEJ
Zn in 6ACO
Zn in 6ACP
Zn in 6ACL
Zn in 6ACE
Zn in 6AA5
Zn in 6ACB
Zn in 6AA3
Zn in 6AA4
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy