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Zinc in PDB 5rme: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z26333434

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z26333434

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z26333434:
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 Z26333434, PDB code: 5rme 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) 81.23 / 2.23
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.049, 70.052, 85.190, 102.84, 95.92, 112.44
R / Rfree (%) 21.2 / 28.4

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 Z26333434 (pdb code 5rme). 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 Z26333434, PDB code: 5rme:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rme

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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 Z26333434


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 Z26333434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:39.2
occ:1.00
 NE2 B:HIS33 2.1 32.9 1.0
ND1 B:HIS39 2.2 46.1 1.0
SG B:CYS16 2.2 46.5 1.0
SG B:CYS19 2.5 36.2 1.0
CD2 B:HIS33 2.9 35.4 1.0
CG B:HIS39 3.0 54.2 1.0
CB B:CYS16 3.1 46.7 1.0
CE1 B:HIS33 3.2 37.9 1.0
CB B:HIS39 3.2 54.3 1.0
CE1 B:HIS39 3.3 51.4 1.0
CB B:CYS19 3.5 38.5 1.0
N B:CYS19 3.5 49.8 1.0
CA B:CYS19 3.9 45.1 1.0
CG B:HIS33 4.1 38.4 1.0
CD2 B:HIS39 4.2 51.6 1.0
ND1 B:HIS33 4.2 37.9 1.0
NE2 B:HIS39 4.3 52.0 1.0
C B:ALA18 4.3 50.6 1.0
CB B:ALA110 4.5 33.5 1.0
CB B:ALA18 4.5 41.0 1.0
CA B:CYS16 4.6 48.9 1.0
CA B:HIS39 4.7 48.6 1.0
CA B:ALA18 4.8 46.6 1.0
N B:ALA18 4.8 49.5 1.0
C B:CYS16 4.9 44.1 1.0

Zinc binding site 2 out of 6 in 5rme

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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 Z26333434


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 Z26333434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:70.3
occ:1.00
 SG B:CYS5 1.8 75.7 1.0
SG B:CYS26 2.2 0.6 1.0
SG B:CYS29 2.4 62.0 1.0
CB B:CYS26 2.9 76.7 1.0
CB B:CYS8 2.9 75.9 1.0
CB B:CYS5 2.9 76.7 1.0
CB B:CYS29 3.1 50.0 1.0
SG B:CYS8 3.3 81.7 1.0
N B:CYS8 3.7 73.6 1.0
N B:CYS26 3.7 87.8 1.0
CA B:CYS26 3.8 81.5 1.0
CA B:CYS8 3.8 75.4 1.0
N B:CYS29 4.3 55.2 1.0
CA B:CYS5 4.3 79.0 1.0
CA B:CYS29 4.3 49.8 1.0
CB B:SER10 4.3 70.4 1.0
O B:CYS26 4.4 83.2 1.0
C B:CYS26 4.5 81.7 1.0
CB B:LEU7 4.6 88.5 1.0
N B:GLY99 4.6 87.0 1.0
C B:LEU7 4.7 73.0 1.0
C B:CYS8 4.7 69.6 1.0
CA B:GLY99 4.8 72.9 1.0
N B:ASN9 4.8 71.3 1.0
C B:CYS5 4.9 75.1 1.0
OG B:SER10 4.9 70.9 1.0
N B:LEU7 4.9 67.5 1.0
O B:GLY99 4.9 60.8 1.0
C B:LEU25 4.9 78.4 1.0
CA B:LEU7 5.0 78.1 1.0

Zinc binding site 3 out of 6 in 5rme

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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 Z26333434


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 Z26333434 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:65.3
occ:1.00
 ND1 B:HIS75 2.5 79.3 1.0
SG B:CYS55 2.5 74.2 1.0
SG B:CYS50 2.6 68.4 1.0
SG B:CYS72 2.8 60.7 1.0
CB B:CYS55 2.8 82.9 1.0
CE1 B:HIS75 3.2 79.6 1.0
CB B:CYS50 3.3 75.8 1.0
CG B:HIS75 3.4 70.2 1.0
CB B:CYS72 3.6 56.9 1.0
CB B:ALA52 3.6 84.7 1.0
CB B:HIS75 3.8 72.0 1.0
N B:CYS72 4.0 48.1 1.0
CG2 B:VAL57 4.3 89.0 1.0
NE2 B:HIS75 4.3 81.9 1.0
CA B:CYS55 4.4 83.3 1.0
CD2 B:HIS75 4.4 76.0 1.0
CA B:CYS72 4.4 54.6 1.0
CB B:VAL57 4.6 91.4 1.0
CA B:CYS50 4.7 79.0 1.0
N B:HIS75 4.8 59.0 1.0
CA B:ALA52 4.9 80.5 1.0
C B:CYS55 5.0 87.9 1.0
CA B:HIS75 5.0 67.1 1.0

Zinc binding site 4 out of 6 in 5rme

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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 Z26333434


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 Z26333434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:64.0
occ:1.00
 SG A:CYS55 2.1 62.4 1.0
ND1 A:HIS75 2.2 59.2 1.0
SG A:CYS50 2.3 54.8 1.0
SG A:CYS72 2.5 59.0 1.0
CB A:CYS55 3.0 56.9 1.0
CE1 A:HIS75 3.1 63.8 1.0
CB A:CYS50 3.1 64.1 1.0
CG A:HIS75 3.3 59.2 1.0
CB A:CYS72 3.4 64.0 1.0
CB A:HIS75 3.7 53.0 1.0
N A:CYS72 3.9 54.8 1.0
CB A:ALA52 4.1 54.5 1.0
NE2 A:HIS75 4.3 59.5 1.0
CA A:CYS72 4.3 64.4 1.0
CD2 A:HIS75 4.4 63.6 1.0
CA A:CYS55 4.4 60.5 1.0
CA A:CYS50 4.6 64.3 1.0
CG2 A:VAL57 4.6 63.4 1.0
CB A:VAL57 4.7 58.6 1.0
N A:HIS75 4.9 54.8 1.0
CA A:HIS75 5.0 52.2 1.0

Zinc binding site 5 out of 6 in 5rme

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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 Z26333434


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 Z26333434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:54.2
occ:1.00
 NE2 A:HIS33 1.8 32.7 1.0
ND1 A:HIS39 2.0 78.0 1.0
SG A:CYS16 2.2 78.0 1.0
SG A:CYS19 2.4 59.5 1.0
CE1 A:HIS33 2.6 36.1 1.0
CD2 A:HIS33 2.9 38.0 1.0
CG A:HIS39 3.0 83.8 1.0
CE1 A:HIS39 3.0 80.2 1.0
N A:CYS19 3.2 52.5 1.0
CB A:HIS39 3.3 76.1 1.0
CB A:CYS16 3.3 69.8 1.0
CB A:CYS19 3.6 50.8 1.0
ND1 A:HIS33 3.8 40.7 1.0
CA A:CYS19 3.8 57.1 1.0
CG A:HIS33 3.9 41.1 1.0
CB A:ALA18 4.0 73.6 1.0
C A:ALA18 4.1 68.2 1.0
CD2 A:HIS39 4.1 84.9 1.0
NE2 A:HIS39 4.1 70.1 1.0
CA A:ALA18 4.5 70.4 1.0
CB A:ALA110 4.5 62.3 1.0
N A:ALA18 4.7 67.3 1.0
CA A:CYS16 4.7 70.9 1.0
CA A:HIS39 4.7 65.2 1.0
C A:CYS16 5.0 60.9 1.0

Zinc binding site 6 out of 6 in 5rme

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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 Z26333434


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 Z26333434 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.6
occ:1.00
 SG A:CYS26 2.2 0.6 1.0
SG A:CYS5 2.3 82.1 1.0
SG A:CYS8 2.6 0.0 1.0
SG A:CYS29 2.6 90.2 1.0
CB A:CYS29 3.1 0.1 1.0
CB A:CYS26 3.1 93.4 1.0
CB A:CYS5 3.5 92.2 1.0
CB A:CYS8 3.6 0.8 1.0
N A:CYS26 3.7 90.7 1.0
CA A:CYS26 3.9 91.1 1.0
N A:CYS8 4.0 0.8 1.0
O A:CYS26 4.1 98.1 1.0
CB A:LEU7 4.3 0.0 1.0
CA A:CYS29 4.3 98.2 1.0
CA A:CYS8 4.4 0.7 1.0
C A:CYS26 4.4 95.7 1.0
N A:CYS29 4.4 0.5 1.0
C A:LEU7 4.8 0.2 1.0
CA A:CYS5 4.9 95.8 1.0
C A:LEU25 4.9 88.9 1.0
O A:CYS5 4.9 95.2 1.0
CA A:LEU7 5.0 0.3 1.0
N A:LEU7 5.0 99.4 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 07:25:41 2025

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