Atomistry » Zinc » PDB 5rlh-5rml » 5rlu
Atomistry »
  Zinc »
    PDB 5rlh-5rml »
      5rlu »

Zinc in PDB 5rlu: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722:
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 Z744754722, PDB code: 5rlu 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) 81.59 / 2.35
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.209, 70.227, 86.037, 103.13, 96.93, 111.98
R / Rfree (%) 16 / 27.3

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 Z744754722 (pdb code 5rlu). 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 Z744754722, PDB code: 5rlu:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlu

Go back to Zinc Binding Sites List in 5rlu
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:89.9
occ:1.00
 ND1 A:HIS75 2.2 80.8 1.0
SG A:CYS55 2.3 94.5 1.0
SG A:CYS50 2.5 92.6 1.0
SG A:CYS72 2.7 91.9 1.0
CG A:HIS75 3.1 77.8 1.0
CE1 A:HIS75 3.2 78.6 1.0
CB A:CYS50 3.3 98.2 1.0
CB A:CYS55 3.3 96.2 1.0
CB A:HIS75 3.4 75.5 1.0
CB A:CYS72 3.4 88.5 1.0
N A:CYS72 3.7 84.1 1.0
CA A:CYS72 4.1 89.6 1.0
N A:HIS75 4.2 77.4 1.0
CD2 A:HIS75 4.3 76.7 1.0
CG2 A:VAL57 4.3 88.7 1.0
NE2 A:HIS75 4.4 76.7 1.0
CA A:HIS75 4.4 77.5 1.0
CB A:ALA52 4.5 80.1 1.0
CB A:VAL57 4.6 87.7 1.0
CA A:CYS55 4.7 0.7 1.0
CA A:CYS50 4.8 97.9 1.0
CB A:SER74 4.8 80.0 1.0
C A:SER74 4.8 80.2 1.0
C A:CYS72 4.8 90.0 1.0
C A:TYR71 4.9 84.2 1.0

Zinc binding site 2 out of 6 in 5rlu

Go back to Zinc Binding Sites List in 5rlu
Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:89.5
occ:1.00
 NE2 A:HIS33 1.9 87.5 1.0
SG A:CYS16 2.2 0.2 1.0
ND1 A:HIS39 2.3 96.6 1.0
SG A:CYS19 2.4 90.0 1.0
CE1 A:HIS33 2.8 86.0 1.0
CD2 A:HIS33 3.0 89.5 1.0
CG A:HIS39 3.0 98.9 1.0
CE1 A:HIS39 3.2 0.6 1.0
CB A:HIS39 3.3 99.0 1.0
CB A:CYS16 3.4 0.2 1.0
CB A:CYS19 3.6 87.9 1.0
N A:CYS19 3.6 89.2 1.0
CA A:CYS19 3.9 90.3 1.0
ND1 A:HIS33 4.0 88.1 1.0
CG A:HIS33 4.1 90.5 1.0
CD2 A:HIS39 4.1 98.9 1.0
NE2 A:HIS39 4.2 0.6 1.0
CB A:ALA110 4.3 85.0 1.0
C A:ALA18 4.3 92.8 1.0
CB A:ALA18 4.5 95.6 1.0
CA A:CYS16 4.7 0.8 1.0
CA A:ALA18 4.8 97.5 1.0
CA A:HIS39 4.8 97.7 1.0
N A:ALA18 4.9 96.9 1.0
CE2 A:PHE106 4.9 97.1 1.0
CZ A:PHE106 4.9 0.8 1.0

Zinc binding site 3 out of 6 in 5rlu

Go back to Zinc Binding Sites List in 5rlu
Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.3
occ:1.00
 SG A:CYS5 2.2 0.1 1.0
SG A:CYS8 2.7 0.8 1.0
SG A:CYS29 2.7 0.6 1.0
SG A:CYS26 2.9 0.6 1.0
CB A:CYS5 3.1 0.4 1.0
CB A:CYS26 3.2 0.1 1.0
CB A:CYS29 3.3 0.5 1.0
N A:CYS8 3.6 0.8 1.0
N A:CYS26 3.7 0.2 1.0
CB A:CYS8 4.0 0.0 1.0
CA A:CYS26 4.0 0.2 1.0
CA A:CYS8 4.2 0.8 1.0
CB A:LEU7 4.3 0.2 1.0
C A:LEU7 4.3 0.0 1.0
N A:LEU7 4.4 0.1 1.0
CA A:LEU7 4.5 0.2 1.0
CA A:CYS5 4.5 0.1 1.0
CB A:SER10 4.5 0.1 1.0
CA A:CYS29 4.6 0.4 1.0
N A:ASN9 4.6 0.4 1.0
C A:CYS8 4.6 0.4 1.0
N A:SER10 4.6 1.0 1.0
OG A:SER10 4.7 0.5 1.0
N A:CYS29 4.7 0.5 1.0
C A:LEU25 4.8 0.9 1.0
O A:SER10 4.9 0.9 1.0
C A:CYS5 4.9 0.9 1.0
C A:CYS26 5.0 0.7 1.0

Zinc binding site 4 out of 6 in 5rlu

Go back to Zinc Binding Sites List in 5rlu
Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:75.8
occ:1.00
 NE2 B:HIS33 1.9 69.9 1.0
ND1 B:HIS39 2.2 80.0 1.0
SG B:CYS16 2.2 72.7 1.0
SG B:CYS19 2.5 79.9 1.0
CE1 B:HIS33 2.9 68.5 1.0
CG B:HIS39 2.9 80.9 1.0
CD2 B:HIS33 3.0 71.5 1.0
CE1 B:HIS39 3.2 80.3 1.0
CB B:HIS39 3.2 81.1 1.0
CB B:CYS16 3.4 76.5 1.0
N B:CYS19 3.6 75.5 1.0
CB B:CYS19 3.6 75.5 1.0
CA B:CYS19 3.9 78.5 1.0
CD2 B:HIS39 4.0 79.9 1.0
ND1 B:HIS33 4.0 68.7 1.0
NE2 B:HIS39 4.1 79.7 1.0
CG B:HIS33 4.1 70.4 1.0
C B:ALA18 4.2 73.0 1.0
CB B:ALA18 4.4 71.5 1.0
CB B:ALA110 4.4 72.7 1.0
CA B:HIS39 4.7 79.8 1.0
CA B:ALA18 4.7 70.0 1.0
CA B:CYS16 4.8 72.0 1.0
N B:ALA18 4.8 74.8 1.0
O B:ALA18 5.0 76.7 1.0

Zinc binding site 5 out of 6 in 5rlu

Go back to Zinc Binding Sites List in 5rlu
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:85.5
occ:1.00
 SG B:CYS5 2.4 80.5 1.0
SG B:CYS29 2.4 75.8 1.0
SG B:CYS26 2.6 90.7 1.0
SG B:CYS8 2.7 0.7 1.0
CB B:CYS29 3.0 72.3 1.0
CB B:CYS26 3.2 85.0 1.0
CB B:CYS5 3.4 87.5 1.0
N B:CYS26 3.7 84.0 1.0
N B:CYS8 3.8 98.0 1.0
CA B:CYS26 4.0 87.0 1.0
CB B:CYS8 4.1 98.7 1.0
CA B:CYS29 4.3 75.9 1.0
CB B:LEU7 4.3 90.8 1.0
N B:CYS29 4.4 79.1 1.0
CA B:CYS8 4.4 98.0 1.0
C B:LEU7 4.5 97.3 1.0
N B:GLY99 4.6 0.1 1.0
CB B:SER10 4.6 92.7 1.0
N B:LEU7 4.6 87.3 1.0
CA B:LEU7 4.7 88.8 1.0
CA B:GLY99 4.7 99.8 1.0
OG B:SER10 4.7 89.8 1.0
C B:GLY99 4.8 98.9 1.0
O B:GLY99 4.8 95.9 1.0
CA B:CYS5 4.8 87.2 1.0
C B:CYS26 4.9 90.1 1.0
C B:LEU25 4.9 84.6 1.0
C B:CYS8 4.9 97.7 1.0
N B:SER10 4.9 0.6 1.0
N B:ASN9 5.0 0.1 1.0

Zinc binding site 6 out of 6 in 5rlu

Go back to Zinc Binding Sites List in 5rlu
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z744754722


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 Z744754722 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:1.0
occ:1.00
 SG B:CYS50 2.2 0.8 1.0
ND1 B:HIS75 2.4 0.5 1.0
SG B:CYS55 2.7 0.5 1.0
SG B:CYS72 2.9 0.8 1.0
CG B:HIS75 3.1 0.5 1.0
CB B:HIS75 3.1 0.9 1.0
CB B:CYS50 3.2 0.6 1.0
N B:CYS72 3.5 0.4 1.0
CB B:CYS72 3.5 0.8 1.0
CB B:CYS55 3.5 0.1 1.0
CE1 B:HIS75 3.5 0.1 1.0
N B:HIS75 3.9 0.1 1.0
CA B:CYS72 4.0 0.4 1.0
CB B:ALA52 4.1 0.4 1.0
CA B:HIS75 4.1 0.5 1.0
CD2 B:HIS75 4.3 1.0 1.0
NE2 B:HIS75 4.5 1.0 1.0
C B:SER74 4.6 0.2 1.0
C B:TYR71 4.6 0.3 1.0
C B:CYS72 4.6 0.5 1.0
CA B:CYS50 4.6 0.0 1.0
CA B:TYR71 4.7 0.2 1.0
CG2 B:VAL57 4.8 0.3 1.0
O B:CYS72 4.8 0.9 1.0
CB B:TYR71 4.9 0.7 1.0
CB B:SER74 4.9 0.4 1.0
CA B:CYS55 5.0 0.3 1.0
CB B:VAL57 5.0 0.7 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 04:06:32 2024

Last articles

Zn in 9MJ5
Zn in 9HNW
Zn in 9G0L
Zn in 9FNE
Zn in 9DZN
Zn in 9E0I
Zn in 9D32
Zn in 9DAK
Zn in 8ZXC
Zn in 8ZUF
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy