Atomistry » Zinc » PDB 5rli-5rmm » 5rm5
Atomistry »
  Zinc »
    PDB 5rli-5rmm »
      5rm5 »

Zinc in PDB 5rm5: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900:
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 Z373768900, PDB code: 5rm5 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) 81.15 / 2.06
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.094, 70.181, 85.187, 103.00, 95.97, 112.29
R / Rfree (%) 20.6 / 26.2

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 Z373768900 (pdb code 5rm5). 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 Z373768900, PDB code: 5rm5:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm5

Go back to Zinc Binding Sites List in 5rm5
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:51.2
occ:1.00
 ND1 A:HIS75 2.2 45.1 1.0
SG A:CYS55 2.2 55.4 1.0
SG A:CYS50 2.2 51.3 1.0
SG A:CYS72 2.5 48.4 1.0
CE1 A:HIS75 3.1 45.0 1.0
CG A:HIS75 3.1 44.0 1.0
CB A:CYS55 3.2 51.2 1.0
CB A:CYS50 3.2 55.3 1.0
CB A:CYS72 3.3 51.3 1.0
CB A:HIS75 3.4 46.2 1.0
N A:CYS72 3.8 51.4 1.0
CB A:ALA52 4.1 55.6 1.0
CA A:CYS72 4.1 52.4 1.0
NE2 A:HIS75 4.2 43.4 1.0
CD2 A:HIS75 4.3 42.8 1.0
CG2 A:VAL57 4.5 64.5 1.0
N A:HIS75 4.6 50.6 1.0
CA A:CYS55 4.6 56.2 1.0
CA A:HIS75 4.6 45.8 1.0
CA A:CYS50 4.7 54.7 1.0
CB A:VAL57 4.7 62.2 1.0
C A:CYS72 4.9 60.6 1.0
CB A:SER74 4.9 57.8 1.0
C A:TYR71 5.0 47.1 1.0

Zinc binding site 2 out of 6 in 5rm5

Go back to Zinc Binding Sites List in 5rm5
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:56.3
occ:1.00
 NE2 A:HIS33 1.8 32.6 1.0
ND1 A:HIS39 2.0 62.7 1.0
SG A:CYS16 2.1 82.6 1.0
SG A:CYS19 2.4 53.9 1.0
CE1 A:HIS33 2.8 40.4 1.0
CD2 A:HIS33 2.9 40.5 1.0
CE1 A:HIS39 3.0 69.5 1.0
CG A:HIS39 3.0 72.0 1.0
N A:CYS19 3.2 52.2 1.0
CB A:CYS16 3.2 76.0 1.0
CB A:HIS39 3.4 66.4 1.0
CB A:CYS19 3.6 40.3 1.0
CA A:CYS19 3.8 49.4 1.0
ND1 A:HIS33 3.9 43.0 1.0
CG A:HIS33 4.0 41.9 1.0
C A:ALA18 4.1 64.8 1.0
NE2 A:HIS39 4.1 68.5 1.0
CB A:ALA18 4.2 74.2 1.0
CD2 A:HIS39 4.2 76.7 1.0
CB A:ALA110 4.4 62.9 1.0
CA A:ALA18 4.5 70.2 1.0
CA A:CYS16 4.6 70.5 1.0
N A:ALA18 4.7 62.7 1.0
CE2 A:PHE106 4.8 48.1 1.0
CA A:HIS39 4.8 61.6 1.0
CZ A:PHE106 5.0 49.0 1.0

Zinc binding site 3 out of 6 in 5rm5

Go back to Zinc Binding Sites List in 5rm5
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:84.4
occ:1.00
 SG A:CYS5 2.1 87.1 1.0
SG A:CYS8 2.3 0.8 1.0
SG A:CYS29 2.5 74.4 1.0
SG A:CYS26 2.6 82.2 1.0
CB A:CYS26 3.1 78.0 1.0
CB A:CYS29 3.1 84.0 1.0
CB A:CYS5 3.3 91.0 1.0
CB A:CYS8 3.6 0.7 1.0
N A:CYS8 3.7 0.3 1.0
N A:CYS26 3.8 73.3 1.0
CA A:CYS26 3.9 80.1 1.0
CA A:CYS8 4.1 0.1 1.0
CB A:LEU7 4.3 96.0 1.0
CA A:CYS29 4.4 81.1 1.0
N A:CYS29 4.5 76.3 1.0
C A:CYS8 4.5 94.4 1.0
CA A:CYS5 4.6 91.9 1.0
C A:LEU7 4.7 94.0 1.0
C A:CYS26 4.7 90.4 1.0
O A:CYS26 4.7 88.3 1.0
N A:ASN9 4.7 0.7 1.0
CB A:SER10 4.7 86.3 1.0
N A:LEU7 4.8 82.5 1.0
O A:CYS5 4.8 84.4 1.0
CA A:LEU7 4.8 91.7 1.0
C A:CYS5 4.9 94.1 1.0
C A:LEU25 5.0 76.0 1.0

Zinc binding site 4 out of 6 in 5rm5

Go back to Zinc Binding Sites List in 5rm5
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:39.0
occ:1.00
 NE2 B:HIS33 2.0 34.8 1.0
ND1 B:HIS39 2.1 51.1 1.0
SG B:CYS16 2.1 43.8 1.0
SG B:CYS19 2.3 40.9 1.0
CD2 B:HIS33 3.0 35.3 1.0
CE1 B:HIS33 3.0 40.4 1.0
CG B:HIS39 3.0 56.0 1.0
CE1 B:HIS39 3.1 53.4 1.0
CB B:CYS16 3.3 45.9 1.0
CB B:HIS39 3.3 47.7 1.0
CB B:CYS19 3.4 43.3 1.0
N B:CYS19 3.4 51.4 1.0
CA B:CYS19 3.8 45.4 1.0
ND1 B:HIS33 4.1 35.5 1.0
CG B:HIS33 4.1 38.0 1.0
NE2 B:HIS39 4.2 52.8 1.0
CD2 B:HIS39 4.2 52.2 1.0
C B:ALA18 4.3 52.3 1.0
CB B:ALA110 4.5 40.0 1.0
CB B:ALA18 4.6 42.1 1.0
CA B:CYS16 4.7 45.5 1.0
CA B:ALA18 4.8 47.4 1.0
CA B:HIS39 4.8 47.1 1.0
N B:ALA18 4.9 48.2 1.0
CE2 B:PHE106 5.0 39.5 1.0

Zinc binding site 5 out of 6 in 5rm5

Go back to Zinc Binding Sites List in 5rm5
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:58.7
occ:1.00
 SG B:CYS26 2.1 63.6 1.0
SG B:CYS29 2.2 54.1 1.0
SG B:CYS5 2.3 62.2 1.0
CB B:CYS29 2.9 49.5 1.0
CB B:CYS8 3.0 74.4 1.0
SG B:CYS8 3.2 80.4 1.0
CB B:CYS26 3.4 61.8 1.0
CB B:CYS5 3.4 68.5 1.0
N B:CYS26 3.8 65.6 1.0
N B:CYS8 3.8 77.7 1.0
CA B:CYS8 4.0 79.3 1.0
N B:CYS29 4.1 51.4 1.0
CA B:CYS29 4.1 49.2 1.0
CA B:CYS26 4.1 68.4 1.0
CB B:LEU7 4.5 82.1 1.0
C B:LEU7 4.6 79.2 1.0
O B:CYS26 4.7 66.9 1.0
CB B:SER10 4.7 64.9 1.0
N B:GLY99 4.7 66.0 1.0
OG B:SER10 4.7 69.7 1.0
C B:CYS26 4.7 69.8 1.0
CA B:GLY99 4.8 62.2 1.0
CA B:CYS5 4.8 71.8 1.0
CA B:LEU7 4.9 80.0 1.0
C B:LEU25 4.9 63.4 1.0
N B:LEU7 5.0 64.7 1.0

Zinc binding site 6 out of 6 in 5rm5

Go back to Zinc Binding Sites List in 5rm5
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z373768900


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 Z373768900 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:73.0
occ:1.00
 SG B:CYS50 2.2 67.9 1.0
SG B:CYS55 2.3 77.5 1.0
ND1 B:HIS75 2.4 86.6 1.0
SG B:CYS72 2.7 61.7 1.0
CB B:CYS55 3.0 86.8 1.0
CB B:CYS50 3.1 66.7 1.0
CG B:HIS75 3.3 83.1 1.0
CB B:HIS75 3.4 75.4 1.0
CE1 B:HIS75 3.5 86.7 1.0
CB B:CYS72 3.6 59.2 1.0
N B:CYS72 3.9 56.6 1.0
CB B:ALA52 4.0 85.7 1.0
CG2 B:VAL57 4.3 70.8 1.0
CA B:CYS72 4.3 61.0 1.0
CD2 B:HIS75 4.5 87.5 1.0
N B:HIS75 4.5 62.0 1.0
CA B:CYS50 4.5 72.2 1.0
CA B:CYS55 4.5 87.9 1.0
NE2 B:HIS75 4.5 84.9 1.0
CA B:HIS75 4.6 72.2 1.0
CB B:VAL57 4.7 75.3 1.0
N B:ALA52 5.0 85.5 1.0
C B:CYS50 5.0 82.9 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 07:22:35 2025

Last articles

Zn in 6JET
Zn in 6JES
Zn in 6JER
Zn in 6JED
Zn in 6JEB
Zn in 6JEA
Zn in 6JDR
Zn in 6JDU
Zn in 6JDS
Zn in 6JE8
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy