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Zinc in PDB 5rlv: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2467208649

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2467208649

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z2467208649:
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 Z2467208649, PDB code: 5rlv 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) 81.60 / 2.21
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.076, 70.270, 85.688, 102.70, 96.47, 112.26
R / Rfree (%) 20.1 / 26

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 Z2467208649 (pdb code 5rlv). 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 Z2467208649, PDB code: 5rlv:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlv

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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 Z2467208649


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 Z2467208649 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:56.3
occ:1.00
 ND1 A:HIS75 2.1 56.8 1.0
SG A:CYS50 2.2 57.3 1.0
SG A:CYS55 2.3 59.0 1.0
SG A:CYS72 2.6 60.1 1.0
CE1 A:HIS75 3.1 58.6 1.0
CG A:HIS75 3.1 51.5 1.0
CB A:CYS50 3.3 67.6 1.0
CB A:CYS55 3.3 60.0 1.0
CB A:HIS75 3.4 50.5 1.0
CB A:CYS72 3.4 60.0 1.0
N A:CYS72 3.9 60.1 1.0
NE2 A:HIS75 4.2 51.7 1.0
CD2 A:HIS75 4.2 49.6 1.0
CA A:CYS72 4.2 61.6 1.0
CB A:ALA52 4.3 54.8 1.0
CA A:HIS75 4.6 51.2 1.0
N A:HIS75 4.6 57.0 1.0
CG2 A:VAL57 4.7 62.2 1.0
CA A:CYS50 4.7 62.6 1.0
CA A:CYS55 4.7 62.6 1.0
CB A:VAL57 4.8 58.9 1.0
C A:CYS72 4.9 68.7 1.0
CB A:SER74 5.0 65.6 1.0
C A:TYR71 5.0 54.4 1.0

Zinc binding site 2 out of 6 in 5rlv

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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 Z2467208649


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 Z2467208649 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:57.4
occ:1.00
 NE2 A:HIS33 1.9 34.1 1.0
ND1 A:HIS39 2.1 83.0 1.0
SG A:CYS16 2.1 88.3 1.0
SG A:CYS19 2.4 62.3 1.0
CE1 A:HIS33 2.8 40.7 1.0
CD2 A:HIS33 3.0 44.6 1.0
CE1 A:HIS39 3.1 87.1 1.0
CG A:HIS39 3.1 83.1 1.0
N A:CYS19 3.1 55.1 1.0
CB A:CYS16 3.2 81.6 1.0
CB A:HIS39 3.4 69.7 1.0
CB A:CYS19 3.5 46.7 1.0
CA A:CYS19 3.7 55.9 1.0
ND1 A:HIS33 3.9 47.5 1.0
C A:ALA18 4.0 65.8 1.0
CG A:HIS33 4.1 47.9 1.0
NE2 A:HIS39 4.2 83.0 1.0
CD2 A:HIS39 4.2 91.5 1.0
CB A:ALA18 4.3 82.8 1.0
CB A:ALA110 4.4 65.0 1.0
CA A:ALA18 4.5 76.0 1.0
CA A:CYS16 4.6 77.8 1.0
N A:ALA18 4.7 64.3 1.0
CA A:HIS39 4.9 67.2 1.0
O A:ALA18 4.9 69.6 1.0
C A:CYS16 5.0 63.3 1.0

Zinc binding site 3 out of 6 in 5rlv

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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 Z2467208649


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 Z2467208649 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn705

b:0.4
occ:1.00
 SG A:CYS5 2.0 84.7 1.0
SG A:CYS8 2.3 0.3 1.0
SG A:CYS29 2.5 90.5 1.0
SG A:CYS26 2.6 96.1 1.0
CB A:CYS26 3.1 91.5 1.0
CB A:CYS5 3.2 88.5 1.0
CB A:CYS29 3.3 97.2 1.0
CB A:CYS8 3.7 0.6 1.0
N A:CYS8 3.7 0.1 1.0
N A:CYS26 3.7 87.5 1.0
CA A:CYS26 4.0 95.7 1.0
CA A:CYS8 4.1 0.1 1.0
CB A:LEU7 4.4 86.0 1.0
C A:CYS8 4.5 0.5 1.0
CA A:CYS5 4.5 92.4 1.0
O A:CYS5 4.5 85.5 1.0
CA A:CYS29 4.6 97.8 1.0
N A:ASN9 4.6 0.5 1.0
C A:CYS5 4.7 96.7 1.0
N A:CYS29 4.7 0.8 1.0
C A:LEU7 4.7 0.1 1.0
CB A:SER10 4.7 90.1 1.0
C A:CYS26 4.7 0.6 1.0
N A:LEU7 4.7 77.3 1.0
O A:CYS26 4.8 0.5 1.0
CA A:LEU7 4.9 87.8 1.0
C A:LEU25 4.9 86.6 1.0

Zinc binding site 4 out of 6 in 5rlv

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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 Z2467208649


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 Z2467208649 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:44.2
occ:1.00
 NE2 B:HIS33 2.0 40.0 1.0
ND1 B:HIS39 2.1 59.9 1.0
SG B:CYS16 2.2 45.3 1.0
SG B:CYS19 2.3 44.9 1.0
CD2 B:HIS33 3.0 35.7 1.0
CE1 B:HIS33 3.0 42.6 1.0
CG B:HIS39 3.1 62.5 1.0
CE1 B:HIS39 3.1 61.2 1.0
CB B:CYS16 3.3 51.8 1.0
CB B:HIS39 3.3 57.9 1.0
CB B:CYS19 3.4 45.3 1.0
N B:CYS19 3.5 54.2 1.0
CA B:CYS19 3.8 49.4 1.0
ND1 B:HIS33 4.1 38.4 1.0
CG B:HIS33 4.1 41.6 1.0
NE2 B:HIS39 4.2 59.6 1.0
CD2 B:HIS39 4.2 57.6 1.0
C B:ALA18 4.3 54.8 1.0
CB B:ALA110 4.5 37.0 1.0
CB B:ALA18 4.6 49.3 1.0
CA B:CYS16 4.7 51.6 1.0
CA B:HIS39 4.8 52.0 1.0
CA B:ALA18 4.9 53.4 1.0
N B:ALA18 5.0 53.1 1.0
CE2 B:PHE106 5.0 44.6 1.0

Zinc binding site 5 out of 6 in 5rlv

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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 Z2467208649


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 Z2467208649 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:63.4
occ:1.00
 SG B:CYS29 2.2 48.1 1.0
SG B:CYS26 2.3 62.8 1.0
SG B:CYS5 2.3 67.8 1.0
CB B:CYS29 2.9 48.5 1.0
CB B:CYS8 3.0 78.2 1.0
SG B:CYS8 3.2 95.5 1.0
CB B:CYS5 3.4 74.8 1.0
CB B:CYS26 3.4 57.8 1.0
N B:CYS8 3.8 84.1 1.0
N B:CYS26 3.9 65.0 1.0
CA B:CYS8 4.0 83.6 1.0
N B:CYS29 4.1 49.6 1.0
CA B:CYS29 4.1 46.5 1.0
CA B:CYS26 4.2 66.0 1.0
CB B:LEU7 4.4 81.1 1.0
C B:LEU7 4.5 83.3 1.0
OG B:SER10 4.7 73.0 1.0
CA B:CYS5 4.8 74.0 1.0
N B:GLY99 4.8 74.7 1.0
C B:CYS26 4.8 69.5 1.0
O B:CYS26 4.9 65.4 1.0
CA B:LEU7 4.9 78.3 1.0
CB B:SER10 4.9 75.9 1.0
CA B:GLY99 4.9 69.0 1.0
N B:LEU7 4.9 67.8 1.0
C B:CYS8 5.0 79.7 1.0

Zinc binding site 6 out of 6 in 5rlv

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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 Z2467208649


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 Z2467208649 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:90.1
occ:1.00
 SG B:CYS50 2.2 84.1 1.0
SG B:CYS55 2.3 92.5 1.0
ND1 B:HIS75 2.5 96.6 1.0
SG B:CYS72 2.9 76.9 1.0
CB B:CYS50 3.0 86.3 1.0
CB B:CYS55 3.3 0.2 1.0
CG B:HIS75 3.3 96.8 1.0
CB B:HIS75 3.3 92.9 1.0
CB B:CYS72 3.5 74.0 1.0
CE1 B:HIS75 3.6 96.6 1.0
N B:CYS72 3.8 67.9 1.0
CB B:ALA52 4.2 88.4 1.0
CA B:CYS72 4.3 76.5 1.0
CG2 B:VAL57 4.3 0.9 1.0
N B:HIS75 4.4 74.7 1.0
CA B:CYS50 4.5 88.9 1.0
CA B:HIS75 4.5 88.7 1.0
CD2 B:HIS75 4.5 96.3 1.0
CB B:VAL57 4.6 0.9 1.0
NE2 B:HIS75 4.7 96.6 1.0
CA B:CYS55 4.7 0.9 1.0
C B:CYS72 4.9 83.6 1.0
C B:TYR71 4.9 75.1 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 04:11:57 2024

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