Atomistry » Zinc » PDB 5rli-5rmm » 5rm6
Atomistry »
  Zinc »
    PDB 5rli-5rmm »
      5rm6 »

Zinc in PDB 5rm6: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540:
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 Z396380540, PDB code: 5rm6 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) 81.58 / 2.13
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.116, 70.245, 85.683, 102.81, 96.39, 112.15
R / Rfree (%) 16.2 / 25.1

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 Z396380540 (pdb code 5rm6). 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 Z396380540, PDB code: 5rm6:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm6

Go back to Zinc Binding Sites List in 5rm6
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:48.9
occ:1.00
 SG A:CYS50 2.4 59.5 1.0
SG A:CYS72 2.5 42.7 1.0
ND1 A:HIS75 2.5 69.3 1.0
SG A:CYS55 2.5 77.9 1.0
CB A:CYS72 3.1 50.7 1.0
CB A:CYS50 3.2 69.5 1.0
CG A:HIS75 3.4 67.1 1.0
CB A:HIS75 3.4 67.8 1.0
N A:CYS72 3.5 55.7 1.0
CE1 A:HIS75 3.6 66.7 1.0
CB A:CYS55 3.6 78.8 1.0
CA A:CYS72 3.9 56.0 1.0
N A:HIS75 4.2 69.1 1.0
CG2 A:VAL57 4.4 75.2 1.0
CA A:HIS75 4.4 68.8 1.0
CB A:ALA52 4.5 63.7 1.0
CD2 A:HIS75 4.6 65.1 1.0
CB A:VAL57 4.6 76.5 1.0
C A:TYR71 4.6 57.4 1.0
C A:CYS72 4.6 62.6 1.0
CA A:CYS50 4.7 69.4 1.0
NE2 A:HIS75 4.7 65.5 1.0
CA A:TYR71 4.9 58.2 1.0
CB A:SER74 5.0 70.0 1.0
O A:CYS72 5.0 65.5 1.0

Zinc binding site 2 out of 6 in 5rm6

Go back to Zinc Binding Sites List in 5rm6
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:72.4
occ:1.00
 NE2 A:HIS33 1.9 71.2 1.0
ND1 A:HIS39 2.2 81.7 1.0
SG A:CYS19 2.3 67.4 1.0
SG A:CYS16 2.4 97.1 1.0
CE1 A:HIS33 2.8 71.6 1.0
CD2 A:HIS33 3.0 72.6 1.0
CG A:HIS39 3.2 83.7 1.0
CE1 A:HIS39 3.2 83.4 1.0
CB A:HIS39 3.4 79.5 1.0
CB A:CYS16 3.4 95.2 1.0
CB A:CYS19 3.6 73.3 1.0
N A:CYS19 3.6 77.8 1.0
CA A:CYS19 3.9 78.5 1.0
ND1 A:HIS33 4.0 73.4 1.0
CG A:HIS33 4.1 74.1 1.0
C A:ALA18 4.2 83.8 1.0
CD2 A:HIS39 4.3 84.6 1.0
NE2 A:HIS39 4.3 84.3 1.0
CB A:ALA110 4.3 68.9 1.0
CB A:ALA18 4.5 86.0 1.0
CA A:ALA18 4.7 87.3 1.0
CA A:CYS16 4.8 95.6 1.0
CE2 A:PHE106 4.9 79.5 1.0
N A:ALA18 4.9 89.1 1.0
O A:ALA18 4.9 84.7 1.0
CA A:HIS39 4.9 76.9 1.0
CZ A:PHE106 5.0 81.9 1.0

Zinc binding site 3 out of 6 in 5rm6

Go back to Zinc Binding Sites List in 5rm6
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.4
occ:1.00
 SG A:CYS5 2.2 0.1 1.0
SG A:CYS8 2.4 0.0 1.0
SG A:CYS26 2.7 0.9 1.0
SG A:CYS29 2.7 0.6 1.0
CB A:CYS26 3.1 0.6 1.0
CB A:CYS5 3.3 0.1 1.0
CB A:CYS29 3.3 0.7 1.0
CB A:CYS8 3.4 0.1 1.0
N A:CYS8 3.4 0.9 1.0
N A:CYS26 3.8 0.9 1.0
CA A:CYS8 3.8 0.2 1.0
CA A:CYS26 4.0 0.2 1.0
C A:LEU7 4.2 0.6 1.0
CB A:LEU7 4.3 0.1 1.0
C A:CYS8 4.4 0.0 1.0
CA A:LEU7 4.6 0.8 1.0
CA A:CYS29 4.6 97.7 1.0
N A:LEU7 4.6 0.9 1.0
N A:CYS29 4.6 0.3 1.0
N A:ASN9 4.7 0.2 1.0
CA A:CYS5 4.7 0.4 1.0
CB A:SER10 4.7 0.6 1.0
C A:CYS26 4.8 0.5 1.0
OG A:SER10 4.9 98.8 1.0
N A:SER10 4.9 0.9 1.0
O A:CYS26 4.9 0.8 1.0
C A:LEU25 5.0 98.7 1.0
O A:CYS8 5.0 0.7 1.0

Zinc binding site 4 out of 6 in 5rm6

Go back to Zinc Binding Sites List in 5rm6
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:58.7
occ:1.00
 NE2 B:HIS33 2.0 57.7 1.0
ND1 B:HIS39 2.2 66.5 1.0
SG B:CYS16 2.2 65.7 1.0
SG B:CYS19 2.4 56.2 1.0
CE1 B:HIS33 3.0 57.9 1.0
CD2 B:HIS33 3.1 58.6 1.0
CG B:HIS39 3.1 67.5 1.0
CE1 B:HIS39 3.2 66.3 1.0
CB B:HIS39 3.3 66.4 1.0
CB B:CYS16 3.4 66.9 1.0
N B:CYS19 3.5 61.3 1.0
CB B:CYS19 3.6 57.3 1.0
CA B:CYS19 3.9 60.2 1.0
C B:ALA18 4.1 59.6 1.0
ND1 B:HIS33 4.1 58.4 1.0
CG B:HIS33 4.2 59.5 1.0
CD2 B:HIS39 4.3 67.3 1.0
NE2 B:HIS39 4.3 67.3 1.0
CB B:ALA18 4.4 53.6 1.0
CB B:ALA110 4.6 52.3 1.0
CA B:ALA18 4.6 58.7 1.0
N B:ALA18 4.7 61.2 1.0
CA B:CYS16 4.7 66.8 1.0
CA B:HIS39 4.8 64.8 1.0
O B:ALA18 4.8 63.6 1.0

Zinc binding site 5 out of 6 in 5rm6

Go back to Zinc Binding Sites List in 5rm6
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:95.1
occ:1.00
 SG B:CYS26 2.2 82.2 1.0
SG B:CYS5 2.2 78.3 1.0
SG B:CYS29 2.7 76.9 1.0
CB B:CYS8 2.7 0.3 1.0
CB B:CYS29 3.1 75.2 1.0
CB B:CYS26 3.3 82.0 1.0
CB B:CYS5 3.3 86.4 1.0
SG B:CYS8 3.5 0.6 1.0
N B:CYS8 3.6 0.0 1.0
N B:CYS26 3.7 77.6 1.0
CA B:CYS8 3.8 98.6 1.0
CA B:CYS26 4.1 79.8 1.0
N B:CYS29 4.2 76.7 1.0
CA B:CYS29 4.3 73.2 1.0
C B:LEU7 4.4 96.7 1.0
CB B:LEU7 4.5 91.8 1.0
CB B:SER10 4.6 87.5 1.0
C B:CYS8 4.6 99.4 1.0
OG B:SER10 4.6 84.0 1.0
CA B:CYS5 4.8 86.4 1.0
N B:LEU7 4.8 88.6 1.0
CA B:LEU7 4.8 92.7 1.0
N B:ASN9 4.9 98.3 1.0
C B:LEU25 4.9 76.1 1.0
C B:CYS26 4.9 82.2 1.0
N B:GLY99 4.9 95.8 1.0
N B:SER10 5.0 91.6 1.0

Zinc binding site 6 out of 6 in 5rm6

Go back to Zinc Binding Sites List in 5rm6
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z396380540


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 Z396380540 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:0.7
occ:1.00
 SG B:CYS50 2.2 0.4 1.0
SG B:CYS55 2.4 0.3 1.0
ND1 B:HIS75 2.5 0.9 1.0
SG B:CYS72 2.8 94.7 1.0
CB B:CYS50 3.0 0.8 1.0
CB B:CYS72 3.3 89.4 1.0
CB B:CYS55 3.4 0.1 1.0
CG B:HIS75 3.4 0.6 1.0
CB B:HIS75 3.5 99.7 1.0
N B:CYS72 3.6 90.3 1.0
CE1 B:HIS75 3.6 0.0 1.0
CA B:CYS72 4.0 91.2 1.0
CB B:ALA52 4.3 0.7 1.0
N B:HIS75 4.4 96.2 1.0
CA B:CYS50 4.5 0.3 1.0
CG2 B:VAL57 4.5 96.9 1.0
CA B:HIS75 4.6 97.0 1.0
CB B:VAL57 4.6 97.6 1.0
CD2 B:HIS75 4.6 0.2 1.0
NE2 B:HIS75 4.7 0.0 1.0
C B:TYR71 4.7 89.4 1.0
CA B:CYS55 4.8 0.4 1.0
C B:CYS72 4.9 92.1 1.0
CA B:TYR71 4.9 93.6 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: Thu Aug 21 07:22:35 2025

Last articles

Zn in 6AK4
Zn in 6AJD
Zn in 6AH3
Zn in 6AHU
Zn in 6AHR
Zn in 6AGO
Zn in 6AEM
Zn in 6AGG
Zn in 6AGB
Zn in 6AEL
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy