Atomistry » Zinc » PDB 5rl8-5rmd » 5rln
Atomistry »
  Zinc »
    PDB 5rl8-5rmd »
      5rln »

Zinc in PDB 5rln: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788:
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 Z364328788, PDB code: 5rln 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) 62.34 / 2.15
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.108, 70.366, 85.925, 102.79, 96.70, 112.26
R / Rfree (%) 17.4 / 25.8

Other elements in 5rln:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788 also contains other interesting chemical elements:

Fluorine (F) 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 Z364328788 (pdb code 5rln). 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 Z364328788, PDB code: 5rln:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:58.4
occ:1.00
 ND1 A:HIS75 2.3 53.5 1.0
SG A:CYS55 2.3 59.8 1.0
SG A:CYS50 2.4 62.3 1.0
SG A:CYS72 2.7 61.0 1.0
CG A:HIS75 3.2 53.4 1.0
CE1 A:HIS75 3.3 53.4 1.0
CB A:CYS50 3.3 66.5 1.0
CB A:CYS55 3.4 65.6 1.0
CB A:CYS72 3.4 61.5 1.0
CB A:HIS75 3.5 51.3 1.0
N A:CYS72 3.8 56.9 1.0
CA A:CYS72 4.2 59.0 1.0
CB A:ALA52 4.2 56.2 1.0
CD2 A:HIS75 4.4 52.5 1.0
NE2 A:HIS75 4.4 51.1 1.0
N A:HIS75 4.4 53.8 1.0
CG2 A:VAL57 4.5 60.7 1.0
CA A:HIS75 4.6 53.3 1.0
CB A:VAL57 4.7 63.8 1.0
CA A:CYS50 4.7 66.6 1.0
CA A:CYS55 4.8 68.3 1.0
C A:TYR71 4.9 53.6 1.0
C A:CYS72 4.9 61.5 1.0

Zinc binding site 2 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:69.5
occ:1.00
 NE2 A:HIS33 2.1 57.4 1.0
ND1 A:HIS39 2.2 79.5 1.0
SG A:CYS19 2.3 71.3 1.0
SG A:CYS16 2.3 86.1 1.0
CE1 A:HIS33 2.9 60.5 1.0
CG A:HIS39 3.2 80.2 1.0
CE1 A:HIS39 3.2 80.5 1.0
CD2 A:HIS33 3.2 63.2 1.0
CB A:CYS19 3.4 71.5 1.0
N A:CYS19 3.4 75.6 1.0
CB A:HIS39 3.4 76.6 1.0
CB A:CYS16 3.4 90.0 1.0
CA A:CYS19 3.7 76.0 1.0
C A:ALA18 4.0 78.9 1.0
ND1 A:HIS33 4.1 65.0 1.0
CG A:HIS33 4.2 66.8 1.0
CD2 A:HIS39 4.3 81.3 1.0
NE2 A:HIS39 4.3 81.3 1.0
CB A:ALA18 4.3 81.2 1.0
CB A:ALA110 4.4 67.0 1.0
CA A:ALA18 4.5 80.5 1.0
O A:ALA18 4.6 78.2 1.0
N A:ALA18 4.7 78.9 1.0
CA A:CYS16 4.8 89.2 1.0
CA A:HIS39 4.9 71.4 1.0

Zinc binding site 3 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.5
occ:1.00
 SG A:CYS5 2.2 99.4 1.0
SG A:CYS26 2.4 0.6 1.0
SG A:CYS8 2.7 1.0 1.0
SG A:CYS29 3.1 94.4 1.0
CB A:CYS29 3.1 0.1 1.0
CB A:CYS5 3.5 0.6 1.0
N A:CYS8 3.6 0.4 1.0
CB A:CYS26 3.7 0.7 1.0
CB A:CYS8 3.8 0.9 1.0
N A:CYS26 4.0 0.2 1.0
CB A:LEU7 4.0 0.6 1.0
CA A:CYS8 4.2 0.4 1.0
C A:LEU7 4.2 0.3 1.0
CA A:CYS26 4.4 0.6 1.0
CA A:CYS29 4.4 98.2 1.0
CA A:LEU7 4.4 0.8 1.0
N A:LEU7 4.5 0.8 1.0
N A:CYS29 4.5 0.4 1.0
CG A:LEU7 4.8 0.3 1.0
C A:CYS8 4.8 0.9 1.0
CA A:CYS5 4.9 0.9 1.0
CD1 A:LEU7 5.0 0.4 1.0

Zinc binding site 4 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:55.3
occ:1.00
 NE2 B:HIS33 2.0 52.0 1.0
ND1 B:HIS39 2.2 51.5 1.0
SG B:CYS16 2.3 56.9 1.0
SG B:CYS19 2.4 54.7 1.0
CE1 B:HIS33 2.9 51.5 1.0
CD2 B:HIS33 3.1 50.8 1.0
CG B:HIS39 3.1 55.7 1.0
CE1 B:HIS39 3.2 52.0 1.0
CB B:HIS39 3.3 55.7 1.0
CB B:CYS16 3.4 56.5 1.0
N B:CYS19 3.4 55.4 1.0
CB B:CYS19 3.5 53.9 1.0
CA B:CYS19 3.8 53.7 1.0
C B:ALA18 4.0 54.5 1.0
ND1 B:HIS33 4.1 51.4 1.0
CG B:HIS33 4.2 51.6 1.0
CD2 B:HIS39 4.3 54.7 1.0
NE2 B:HIS39 4.3 52.7 1.0
CB B:ALA18 4.4 50.8 1.0
CB B:ALA110 4.5 46.4 1.0
CA B:ALA18 4.6 53.1 1.0
N B:ALA18 4.7 54.4 1.0
O B:ALA18 4.7 53.4 1.0
CA B:CYS16 4.7 57.6 1.0
CA B:HIS39 4.8 54.7 1.0
C B:CYS16 5.0 57.4 1.0

Zinc binding site 5 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:73.7
occ:1.00
 SG B:CYS26 2.2 63.8 1.0
SG B:CYS5 2.3 64.9 1.0
SG B:CYS29 2.5 68.7 1.0
CB B:CYS8 2.9 84.4 1.0
CB B:CYS29 3.0 58.6 1.0
SG B:CYS8 3.0 88.0 1.0
CB B:CYS26 3.4 62.8 1.0
CB B:CYS5 3.5 70.6 1.0
N B:CYS8 3.9 77.2 1.0
N B:CYS26 3.9 63.6 1.0
CA B:CYS8 4.0 79.6 1.0
N B:CYS29 4.1 61.5 1.0
CA B:CYS29 4.1 59.2 1.0
CA B:CYS26 4.2 63.1 1.0
CB B:LEU7 4.5 72.0 1.0
N B:GLY99 4.5 80.4 1.0
C B:LEU7 4.6 76.1 1.0
CA B:GLY99 4.6 81.5 1.0
OG B:SER10 4.7 75.5 1.0
CB B:SER10 4.9 75.9 1.0
CA B:LEU7 4.9 74.0 1.0
N B:LEU7 4.9 73.0 1.0
C B:CYS26 4.9 64.5 1.0
CA B:CYS5 4.9 71.6 1.0
O B:CYS26 5.0 64.6 1.0
C B:GLY99 5.0 79.0 1.0

Zinc binding site 6 out of 6 in 5rln

Go back to Zinc Binding Sites List in 5rln
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z364328788


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 Z364328788 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:90.9
occ:1.00
 SG B:CYS50 2.2 88.9 1.0
ND1 B:HIS75 2.4 0.1 1.0
SG B:CYS55 2.5 0.6 1.0
SG B:CYS72 2.9 83.4 1.0
CB B:CYS55 3.1 0.6 1.0
CB B:CYS50 3.1 98.4 1.0
CG B:HIS75 3.3 0.4 1.0
CE1 B:HIS75 3.4 0.8 1.0
CB B:CYS72 3.5 78.7 1.0
CB B:HIS75 3.5 0.7 1.0
N B:CYS72 3.8 80.5 1.0
CB B:ALA52 4.0 0.3 1.0
CA B:CYS72 4.2 79.9 1.0
CG2 B:VAL57 4.5 89.3 1.0
CD2 B:HIS75 4.5 0.8 1.0
CA B:CYS50 4.5 95.8 1.0
NE2 B:HIS75 4.5 0.3 1.0
CA B:CYS55 4.5 0.2 1.0
N B:HIS75 4.6 92.9 1.0
CB B:VAL57 4.7 90.0 1.0
CA B:HIS75 4.7 96.6 1.0
C B:TYR71 4.9 81.3 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: Wed Dec 16 07:14:35 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy