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Zinc in PDB 5rmj: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550:
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 Z68299550, PDB code: 5rmj 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 / 2.10
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 58.840, 70.136, 85.256, 103.14, 95.74, 112.26
R / Rfree (%) 23.3 / 29.7

Other elements in 5rmj:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

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 Z68299550 (pdb code 5rmj). 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 Z68299550, PDB code: 5rmj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmj

Go back to Zinc Binding Sites List in 5rmj
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550


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 Z68299550 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:42.3
occ:1.00
NE2 B:HIS33 2.1 38.0 1.0
ND1 B:HIS39 2.1 43.4 1.0
SG B:CYS16 2.2 44.9 1.0
SG B:CYS19 2.5 44.8 1.0
CG B:HIS39 2.9 51.0 1.0
CD2 B:HIS33 3.0 37.7 1.0
CE1 B:HIS39 3.1 46.3 1.0
CE1 B:HIS33 3.2 38.0 1.0
CB B:HIS39 3.2 51.5 1.0
CB B:CYS16 3.2 46.2 1.0
N B:CYS19 3.3 53.4 1.0
CB B:CYS19 3.4 45.4 1.0
CA B:CYS19 3.8 48.0 1.0
CD2 B:HIS39 3.9 48.3 1.0
NE2 B:HIS39 4.0 45.5 1.0
C B:ALA18 4.2 50.3 1.0
CG B:HIS33 4.2 40.1 1.0
ND1 B:HIS33 4.3 40.0 1.0
CB B:ALA18 4.4 43.0 1.0
CB B:ALA110 4.6 42.4 1.0
CA B:CYS16 4.6 46.4 1.0
CA B:ALA18 4.7 48.5 1.0
CA B:HIS39 4.7 49.5 1.0
N B:ALA18 4.8 48.1 1.0
O B:ALA18 5.0 49.6 1.0

Zinc binding site 2 out of 6 in 5rmj

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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 Z68299550


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 Z68299550 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:66.2
occ:1.00
SG B:CYS5 1.7 0.2 1.0
SG B:CYS26 1.8 0.6 1.0
SG B:CYS29 2.4 60.1 1.0
CB B:CYS5 2.6 0.8 1.0
CB B:CYS26 2.7 79.5 1.0
CB B:CYS8 3.1 1.0 1.0
CB B:CYS29 3.2 56.1 1.0
N B:CYS26 3.5 86.5 1.0
CA B:CYS26 3.6 86.9 1.0
SG B:CYS8 3.7 0.1 1.0
N B:CYS8 3.9 0.6 1.0
CA B:CYS5 4.0 97.2 1.0
CB B:SER10 4.0 80.6 1.0
CA B:CYS8 4.1 0.3 1.0
O B:CYS26 4.1 98.4 1.0
N B:CYS29 4.2 61.9 1.0
C B:CYS26 4.3 92.4 1.0
CA B:CYS29 4.3 55.5 1.0
C B:CYS5 4.6 93.4 1.0
O B:CYS5 4.6 92.4 1.0
OG B:SER10 4.6 93.2 1.0
C B:LEU25 4.7 75.1 1.0
N B:ASN9 4.8 79.0 1.0
O B:SER10 4.8 99.1 1.0
N B:GLY99 4.9 81.6 1.0
C B:CYS8 4.9 91.2 1.0
N B:SER10 4.9 76.0 1.0
CB B:LEU7 5.0 0.7 1.0
CA B:SER10 5.0 84.9 1.0
C B:LEU7 5.0 0.1 1.0

Zinc binding site 3 out of 6 in 5rmj

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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 Z68299550


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 Z68299550 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:78.3
occ:1.00
ND1 B:HIS75 2.3 90.1 1.0
SG B:CYS55 2.4 81.8 1.0
SG B:CYS50 2.4 88.7 1.0
SG B:CYS72 2.7 71.8 1.0
CB B:CYS55 2.9 96.3 1.0
CE1 B:HIS75 3.2 86.9 1.0
CG B:HIS75 3.2 84.1 1.0
CB B:CYS50 3.4 87.9 1.0
CB B:CYS72 3.4 69.2 1.0
CB B:HIS75 3.5 80.7 1.0
CB B:ALA52 3.8 0.9 1.0
N B:CYS72 3.9 64.6 1.0
NE2 B:HIS75 4.2 85.5 1.0
CD2 B:HIS75 4.2 83.1 1.0
CA B:CYS72 4.2 71.1 1.0
CA B:CYS55 4.4 98.8 1.0
CG2 B:VAL57 4.4 80.1 1.0
N B:HIS75 4.6 69.2 1.0
CA B:HIS75 4.7 77.0 1.0
CB B:VAL57 4.7 82.0 1.0
CA B:CYS50 4.8 88.7 1.0
C B:CYS72 4.8 81.9 1.0
C B:CYS55 5.0 99.1 1.0
O B:CYS72 5.0 83.8 1.0

Zinc binding site 4 out of 6 in 5rmj

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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 Z68299550


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 Z68299550 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:62.8
occ:1.00
SG A:CYS55 2.2 62.0 1.0
SG A:CYS50 2.3 64.5 1.0
ND1 A:HIS75 2.3 55.0 1.0
SG A:CYS72 2.4 49.8 1.0
CB A:CYS55 3.1 55.3 1.0
CE1 A:HIS75 3.2 59.3 1.0
CB A:CYS50 3.3 67.3 1.0
CG A:HIS75 3.4 54.1 1.0
CB A:CYS72 3.4 58.6 1.0
CB A:HIS75 3.7 52.5 1.0
N A:CYS72 4.0 54.0 1.0
CB A:ALA52 4.1 58.2 1.0
CA A:CYS72 4.2 59.6 1.0
NE2 A:HIS75 4.4 52.6 1.0
CD2 A:HIS75 4.5 53.1 1.0
CA A:CYS55 4.5 60.0 1.0
CA A:CYS50 4.7 68.7 1.0
CG2 A:VAL57 4.8 61.0 1.0
N A:HIS75 4.8 55.9 1.0
CB A:VAL57 4.8 57.9 1.0
CA A:HIS75 4.9 52.9 1.0
CB A:SER74 4.9 63.3 1.0
C A:CYS72 5.0 62.0 1.0

Zinc binding site 5 out of 6 in 5rmj

Go back to Zinc Binding Sites List in 5rmj
Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550


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 Z68299550 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:57.6
occ:1.00
NE2 A:HIS33 1.7 35.3 1.0
ND1 A:HIS39 2.1 81.4 1.0
SG A:CYS16 2.3 92.0 1.0
SG A:CYS19 2.6 53.7 1.0
CE1 A:HIS33 2.7 40.1 1.0
CD2 A:HIS33 2.8 43.1 1.0
CG A:HIS39 3.0 88.5 1.0
CE1 A:HIS39 3.1 85.8 1.0
N A:CYS19 3.1 53.2 1.0
CB A:HIS39 3.3 79.0 1.0
CB A:CYS16 3.4 90.8 1.0
CB A:CYS19 3.6 45.1 1.0
CA A:CYS19 3.8 50.6 1.0
ND1 A:HIS33 3.8 42.6 1.0
CG A:HIS33 3.9 45.0 1.0
C A:ALA18 4.0 67.2 1.0
CB A:ALA18 4.1 77.2 1.0
CD2 A:HIS39 4.2 90.5 1.0
NE2 A:HIS39 4.2 84.7 1.0
CA A:ALA18 4.4 76.1 1.0
CB A:ALA110 4.5 58.9 1.0
N A:ALA18 4.7 72.2 1.0
CA A:HIS39 4.7 73.8 1.0
CA A:CYS16 4.8 88.0 1.0
O A:ALA18 4.9 78.6 1.0
CE2 A:PHE106 4.9 46.5 1.0

Zinc binding site 6 out of 6 in 5rmj

Go back to Zinc Binding Sites List in 5rmj
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z68299550


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 Z68299550 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.3
occ:1.00
SG A:CYS26 2.3 93.7 1.0
SG A:CYS5 2.4 87.9 1.0
SG A:CYS8 2.5 0.8 1.0
SG A:CYS29 2.5 90.4 1.0
CB A:CYS26 3.0 89.0 1.0
CB A:CYS29 3.1 98.8 1.0
CB A:CYS8 3.5 0.5 1.0
CB A:CYS5 3.6 95.5 1.0
N A:CYS26 3.9 85.0 1.0
CA A:CYS26 3.9 86.7 1.0
N A:CYS8 3.9 0.7 1.0
CA A:CYS8 4.3 0.4 1.0
O A:CYS26 4.3 99.8 1.0
CA A:CYS29 4.4 93.4 1.0
N A:CYS29 4.4 94.8 1.0
CB A:LEU7 4.4 0.0 1.0
C A:CYS26 4.5 95.1 1.0
C A:LEU7 4.8 0.6 1.0
C A:CYS8 4.9 0.4 1.0
CA A:CYS5 4.9 99.4 1.0
CB A:SER10 5.0 97.9 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: Wed Dec 16 08:31:51 2020

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