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

Zinc in PDB 5rmf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006:
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 Z54226006, PDB code: 5rmf 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) 81.49 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.190, 70.107, 85.386, 102.60, 96.01, 112.56
R / Rfree (%) 20.8 / 27

Other elements in 5rmf:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

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 Z54226006 (pdb code 5rmf). 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 Z54226006, PDB code: 5rmf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:55.1
occ:1.00
 SG A:CYS55 2.1 56.7 1.0
SG A:CYS50 2.2 55.9 1.0
ND1 A:HIS75 2.3 53.9 1.0
SG A:CYS72 2.6 52.5 1.0
CB A:CYS50 3.1 58.9 1.0
CB A:CYS55 3.2 56.5 1.0
CE1 A:HIS75 3.2 58.3 1.0
CG A:HIS75 3.3 51.3 1.0
CB A:CYS72 3.3 55.6 1.0
CB A:HIS75 3.6 50.2 1.0
N A:CYS72 3.8 51.6 1.0
CA A:CYS72 4.1 56.5 1.0
NE2 A:HIS75 4.4 54.0 1.0
CB A:ALA52 4.4 56.4 1.0
CD2 A:HIS75 4.4 53.4 1.0
N A:HIS75 4.5 54.1 1.0
CG2 A:VAL57 4.5 53.0 1.0
CA A:CYS50 4.6 55.9 1.0
CA A:CYS55 4.6 59.7 1.0
CB A:VAL57 4.7 52.8 1.0
CA A:HIS75 4.7 49.0 1.0
C A:TYR71 4.9 45.9 1.0
C A:CYS72 4.9 60.3 1.0

Zinc binding site 2 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:51.3
occ:1.00
 NE2 A:HIS33 2.0 34.9 1.0
ND1 A:HIS39 2.1 62.1 1.0
SG A:CYS16 2.2 76.7 1.0
SG A:CYS19 2.3 50.4 1.0
CE1 A:HIS33 2.7 38.6 1.0
CG A:HIS39 3.0 68.5 1.0
CE1 A:HIS39 3.1 66.3 1.0
CD2 A:HIS33 3.2 41.9 1.0
N A:CYS19 3.2 52.7 1.0
CB A:HIS39 3.3 66.6 1.0
CB A:CYS16 3.4 66.8 1.0
CB A:CYS19 3.5 46.7 1.0
CA A:CYS19 3.7 52.9 1.0
ND1 A:HIS33 4.0 43.4 1.0
C A:ALA18 4.1 59.5 1.0
NE2 A:HIS39 4.1 64.7 1.0
CD2 A:HIS39 4.1 72.3 1.0
CB A:ALA18 4.2 67.6 1.0
CG A:HIS33 4.2 45.6 1.0
CB A:ALA110 4.5 51.0 1.0
CA A:ALA18 4.6 63.0 1.0
N A:ALA18 4.7 58.7 1.0
CA A:CYS16 4.7 65.7 1.0
CA A:HIS39 4.8 60.8 1.0
CE2 A:PHE106 4.9 54.4 1.0
CZ A:PHE106 5.0 55.4 1.0

Zinc binding site 3 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:81.2
occ:1.00
 SG A:CYS5 2.2 76.0 1.0
SG A:CYS8 2.3 0.3 1.0
SG A:CYS29 2.4 74.8 1.0
SG A:CYS26 2.6 76.5 1.0
CB A:CYS29 3.0 75.3 1.0
CB A:CYS26 3.1 71.5 1.0
CB A:CYS5 3.4 78.2 1.0
N A:CYS26 3.7 71.6 1.0
CB A:CYS8 3.8 94.2 1.0
N A:CYS8 3.9 95.0 1.0
CA A:CYS26 3.9 73.0 1.0
O A:CYS26 4.2 79.1 1.0
CA A:CYS29 4.3 70.7 1.0
CB A:LEU7 4.3 90.8 1.0
N A:CYS29 4.3 72.2 1.0
CA A:CYS8 4.3 96.5 1.0
C A:CYS26 4.5 78.3 1.0
C A:LEU7 4.7 88.9 1.0
CB A:SER10 4.7 87.5 1.0
CA A:CYS5 4.8 81.1 1.0
N A:LEU7 4.8 75.8 1.0
CA A:LEU7 4.8 85.4 1.0
C A:LEU25 4.9 72.0 1.0
OG A:SER10 4.9 77.0 1.0
C A:CYS8 5.0 93.5 1.0

Zinc binding site 4 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:42.1
occ:1.00
 NE2 B:HIS33 2.0 37.5 1.0
ND1 B:HIS39 2.2 52.6 1.0
SG B:CYS16 2.2 44.2 1.0
SG B:CYS19 2.4 43.2 1.0
CE1 B:HIS33 2.9 38.5 1.0
CD2 B:HIS33 3.0 40.0 1.0
CG B:HIS39 3.1 58.2 1.0
CE1 B:HIS39 3.1 54.0 1.0
CB B:HIS39 3.3 52.0 1.0
N B:CYS19 3.4 54.4 1.0
CB B:CYS16 3.4 54.7 1.0
CB B:CYS19 3.5 40.6 1.0
CA B:CYS19 3.9 47.8 1.0
ND1 B:HIS33 4.1 37.8 1.0
CG B:HIS33 4.1 40.9 1.0
CD2 B:HIS39 4.2 55.1 1.0
NE2 B:HIS39 4.2 55.5 1.0
C B:ALA18 4.3 55.0 1.0
CB B:ALA18 4.4 46.8 1.0
CB B:ALA110 4.4 41.1 1.0
CA B:ALA18 4.7 50.4 1.0
CA B:CYS16 4.8 56.3 1.0
CA B:HIS39 4.8 51.2 1.0
N B:ALA18 4.8 50.1 1.0
CE2 B:PHE106 4.9 44.4 1.0
CZ B:PHE106 5.0 45.8 1.0

Zinc binding site 5 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:75.2
occ:1.00
 SG B:CYS5 2.0 85.6 1.0
SG B:CYS26 2.1 71.1 1.0
SG B:CYS29 2.6 61.5 1.0
CB B:CYS29 2.9 68.3 1.0
CB B:CYS26 3.0 66.5 1.0
CB B:CYS5 3.2 87.1 1.0
SG B:CYS8 3.3 91.7 1.0
N B:CYS26 3.5 82.5 1.0
CB B:CYS8 3.7 91.4 1.0
N B:CYS8 3.8 92.6 1.0
CA B:CYS26 3.8 77.9 1.0
CA B:CYS29 4.2 69.4 1.0
O B:CYS26 4.3 78.3 1.0
CA B:CYS8 4.3 89.8 1.0
N B:CYS29 4.3 74.5 1.0
CB B:LEU7 4.3 94.0 1.0
C B:CYS26 4.5 84.0 1.0
C B:LEU7 4.5 90.2 1.0
CA B:CYS5 4.6 84.9 1.0
OG B:SER10 4.6 63.3 1.0
N B:LEU7 4.6 77.2 1.0
CB B:SER10 4.7 65.5 1.0
C B:LEU25 4.7 79.8 1.0
CA B:LEU7 4.7 90.0 1.0
N B:GLY99 4.9 87.8 1.0
N B:ASN9 5.0 78.0 1.0
CA B:GLY99 5.0 81.1 1.0
CA B:LEU25 5.0 72.0 1.0

Zinc binding site 6 out of 6 in 5rmf

Go back to Zinc Binding Sites List in 5rmf
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z54226006


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 Z54226006 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.9
occ:1.00
 SG B:CYS50 2.2 68.0 1.0
SG B:CYS55 2.2 88.1 1.0
ND1 B:HIS75 2.5 83.5 1.0
SG B:CYS72 2.7 63.8 1.0
CB B:CYS50 3.2 74.8 1.0
CB B:CYS55 3.3 93.3 1.0
CG B:HIS75 3.3 85.1 1.0
CB B:CYS72 3.4 68.0 1.0
CB B:HIS75 3.4 85.2 1.0
CE1 B:HIS75 3.6 85.8 1.0
N B:CYS72 3.7 67.3 1.0
CA B:CYS72 4.1 68.2 1.0
N B:HIS75 4.3 73.3 1.0
CB B:ALA52 4.3 86.2 1.0
CG2 B:VAL57 4.4 0.2 1.0
CA B:HIS75 4.5 82.9 1.0
CD2 B:HIS75 4.5 86.1 1.0
CA B:CYS50 4.6 75.9 1.0
NE2 B:HIS75 4.6 87.2 1.0
CB B:VAL57 4.6 0.1 1.0
CA B:CYS55 4.7 93.8 1.0
C B:CYS72 4.9 71.9 1.0
C B:TYR71 4.9 74.0 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: Mon Oct 28 04:23:17 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