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Zinc in PDB 5rle: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185:
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 Z1429867185, PDB code: 5rle 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) 81.68 / 2.27
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.107, 70.049, 85.840, 103.00, 96.26, 112.24
R / Rfree (%) 15.1 / 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 Z1429867185 (pdb code 5rle). 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 Z1429867185, PDB code: 5rle:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rle

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Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185


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 Z1429867185 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:0.7
occ:1.00
 SG A:CYS50 2.3 93.8 1.0
SG A:CYS55 2.5 0.0 1.0
ND1 A:HIS75 2.6 98.6 1.0
SG A:CYS72 2.9 0.2 1.0
CG A:HIS75 3.3 97.9 1.0
CB A:HIS75 3.4 94.6 1.0
CB A:CYS50 3.5 0.6 1.0
CB A:CYS72 3.5 0.6 1.0
CB A:CYS55 3.6 0.0 1.0
CE1 A:HIS75 3.7 98.5 1.0
N A:CYS72 3.8 96.5 1.0
CB A:ALA52 4.1 89.0 1.0
CA A:CYS72 4.2 98.9 1.0
N A:HIS75 4.4 95.6 1.0
CD2 A:HIS75 4.5 98.2 1.0
CA A:HIS75 4.5 95.4 1.0
NE2 A:HIS75 4.6 93.7 1.0
CG2 A:VAL57 4.7 90.2 1.0
CA A:CYS50 4.9 0.8 1.0
CB A:VAL57 4.9 92.7 1.0
C A:TYR71 4.9 89.9 1.0
C A:CYS72 4.9 0.1 1.0
C A:SER74 5.0 0.5 1.0
CA A:CYS55 5.0 0.3 1.0

Zinc binding site 2 out of 6 in 5rle

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Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185


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 Z1429867185 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:85.1
occ:1.00
 NE2 A:HIS33 2.0 99.4 1.0
SG A:CYS16 2.3 0.6 1.0
SG A:CYS19 2.4 92.3 1.0
ND1 A:HIS39 2.7 0.2 1.0
CD2 A:HIS33 2.9 0.7 1.0
CE1 A:HIS33 3.1 99.4 1.0
CG A:HIS39 3.2 0.5 1.0
CB A:CYS16 3.4 0.8 1.0
CE1 A:HIS39 3.5 0.2 1.0
CB A:HIS39 3.5 0.7 1.0
CB A:CYS19 3.7 91.6 1.0
N A:CYS19 3.9 88.9 1.0
CD2 A:HIS39 4.1 0.5 1.0
CG A:HIS33 4.1 99.5 1.0
CA A:CYS19 4.1 95.5 1.0
ND1 A:HIS33 4.2 99.3 1.0
NE2 A:HIS39 4.2 0.3 1.0
CB A:ALA110 4.2 88.3 1.0
C A:ALA18 4.5 92.1 1.0
CB A:ALA18 4.6 95.8 1.0
CE2 A:PHE106 4.6 95.5 1.0
CA A:CYS16 4.8 0.8 1.0
CZ A:PHE106 4.8 95.2 1.0
CA A:ALA18 4.9 93.2 1.0
CA A:HIS39 5.0 0.2 1.0

Zinc binding site 3 out of 6 in 5rle

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Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185


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 Z1429867185 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.1
occ:1.00
 SG A:CYS29 2.2 0.6 1.0
SG A:CYS26 2.2 0.3 1.0
SG A:CYS8 2.4 0.8 1.0
SG A:CYS5 2.6 0.0 1.0
CB A:CYS29 3.1 0.4 1.0
CB A:CYS8 3.5 0.8 1.0
CB A:CYS26 3.5 0.5 1.0
N A:CYS8 3.8 0.0 1.0
CB A:CYS5 3.9 0.5 1.0
N A:CYS26 4.0 0.5 1.0
CB A:LEU7 4.1 0.9 1.0
CA A:CYS8 4.2 0.4 1.0
N A:CYS29 4.2 1.0 1.0
CA A:CYS29 4.3 0.2 1.0
CA A:CYS26 4.3 0.3 1.0
C A:LEU7 4.3 0.5 1.0
CA A:LEU7 4.7 0.3 1.0
O A:CYS26 4.7 0.3 1.0
C A:CYS26 4.8 0.5 1.0
N A:LEU7 4.9 0.4 1.0
C A:CYS8 5.0 0.7 1.0
O A:LEU7 5.0 0.9 1.0

Zinc binding site 4 out of 6 in 5rle

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Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185


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 Z1429867185 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:80.7
occ:1.00
 NE2 B:HIS33 2.2 82.5 1.0
SG B:CYS16 2.3 79.8 1.0
ND1 B:HIS39 2.5 91.1 1.0
SG B:CYS19 2.5 86.4 1.0
CG B:HIS39 3.0 91.0 1.0
CD2 B:HIS33 3.1 82.2 1.0
CE1 B:HIS33 3.2 83.0 1.0
CE1 B:HIS39 3.3 89.6 1.0
CB B:HIS39 3.3 90.4 1.0
CB B:CYS16 3.4 80.3 1.0
N B:CYS19 3.6 91.1 1.0
CB B:CYS19 3.7 88.2 1.0
CD2 B:HIS39 3.9 90.8 1.0
CA B:CYS19 3.9 92.8 1.0
NE2 B:HIS39 4.0 87.5 1.0
CG B:HIS33 4.3 83.4 1.0
C B:ALA18 4.3 90.3 1.0
ND1 B:HIS33 4.3 82.7 1.0
CB B:ALA18 4.4 85.4 1.0
CB B:ALA110 4.4 69.6 1.0
CA B:ALA18 4.7 89.2 1.0
CA B:HIS39 4.8 88.4 1.0
CA B:CYS16 4.8 82.1 1.0
N B:ALA18 4.8 88.7 1.0
O B:ALA18 5.0 94.1 1.0

Zinc binding site 5 out of 6 in 5rle

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Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185


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 Z1429867185 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:0.1
occ:1.00
 SG B:CYS26 2.2 98.5 1.0
SG B:CYS5 2.2 97.4 1.0
SG B:CYS29 2.5 89.7 1.0
CB B:CYS8 2.8 0.3 1.0
CB B:CYS29 3.2 91.1 1.0
CB B:CYS26 3.3 0.5 1.0
CB B:CYS5 3.4 0.5 1.0
N B:CYS8 3.6 0.6 1.0
SG B:CYS8 3.7 1.0 1.0
N B:CYS26 3.7 0.6 1.0
CA B:CYS8 3.8 0.7 1.0
CA B:CYS26 4.1 99.9 1.0
CB B:LEU7 4.2 1.0 1.0
C B:LEU7 4.3 0.1 1.0
OG B:SER10 4.3 0.7 1.0
CA B:CYS29 4.4 91.4 1.0
N B:CYS29 4.4 97.8 1.0
CB B:SER10 4.5 0.1 1.0
O B:CYS26 4.6 0.4 1.0
CA B:LEU7 4.6 0.2 1.0
C B:CYS8 4.7 0.7 1.0
N B:GLY99 4.7 0.9 1.0
N B:LEU7 4.7 0.8 1.0
C B:CYS26 4.7 0.4 1.0
CA B:CYS5 4.8 0.5 1.0
CA B:GLY99 4.9 0.7 1.0
C B:LEU25 4.9 98.1 1.0
N B:ASN9 4.9 0.1 1.0

Zinc binding site 6 out of 6 in 5rle

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Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z1429867185


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 Z1429867185 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:0.5
occ:1.00
 SG B:CYS50 2.2 0.2 1.0
SG B:CYS55 2.5 0.5 1.0
ND1 B:HIS75 2.7 0.9 1.0
SG B:CYS72 2.9 0.8 1.0
CB B:CYS50 3.3 0.9 1.0
CB B:HIS75 3.4 0.3 1.0
CG B:HIS75 3.4 0.3 1.0
CB B:CYS72 3.5 0.7 1.0
CB B:CYS55 3.6 0.9 1.0
N B:CYS72 3.7 0.7 1.0
CE1 B:HIS75 3.8 0.8 1.0
CB B:ALA52 4.0 0.3 1.0
CA B:CYS72 4.2 0.7 1.0
N B:HIS75 4.4 0.3 1.0
CA B:HIS75 4.5 0.3 1.0
CD2 B:HIS75 4.5 0.4 1.0
CA B:CYS50 4.7 0.5 1.0
NE2 B:HIS75 4.7 0.8 1.0
CG2 B:VAL57 4.8 0.9 1.0
C B:TYR71 4.8 0.3 1.0
CB B:VAL57 4.9 0.7 1.0
C B:CYS72 4.9 0.8 1.0
C B:SER74 5.0 0.1 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 03:59:21 2024

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