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Zinc in PDB 5rm7: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z69118333

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z69118333

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z69118333:
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 Z69118333, PDB code: 5rm7 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) 81.42 / 1.84
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.151, 70.168, 85.300, 102.36, 96.32, 112.51
R / Rfree (%) 22.2 / 26.9

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 Z69118333 (pdb code 5rm7). 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 Z69118333, PDB code: 5rm7:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm7

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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 Z69118333


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 Z69118333 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:51.0
occ:1.00
 SG A:CYS50 2.2 55.6 1.0
SG A:CYS55 2.2 49.4 1.0
ND1 A:HIS75 2.2 49.3 1.0
SG A:CYS72 2.4 53.3 1.0
CG A:HIS75 3.2 45.9 1.0
CB A:CYS50 3.2 58.4 1.0
CE1 A:HIS75 3.2 50.2 1.0
CB A:CYS55 3.2 50.0 1.0
CB A:CYS72 3.3 56.3 1.0
CB A:HIS75 3.4 46.3 1.0
N A:CYS72 3.8 49.7 1.0
CA A:CYS72 4.1 55.2 1.0
CB A:ALA52 4.2 45.9 1.0
CD2 A:HIS75 4.3 43.8 1.0
NE2 A:HIS75 4.3 49.5 1.0
N A:HIS75 4.5 55.2 1.0
CG2 A:VAL57 4.5 56.2 1.0
CA A:HIS75 4.6 50.7 1.0
CA A:CYS50 4.6 54.9 1.0
CA A:CYS55 4.7 53.1 1.0
CB A:VAL57 4.7 57.0 1.0
C A:CYS72 4.7 61.0 1.0
CB A:SER74 4.9 60.4 1.0
O A:CYS72 4.9 58.6 1.0
C A:TYR71 4.9 47.7 1.0

Zinc binding site 2 out of 6 in 5rm7

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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 Z69118333


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 Z69118333 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:50.7
occ:1.00
 NE2 A:HIS33 1.8 26.6 1.0
ND1 A:HIS39 2.1 68.3 1.0
SG A:CYS16 2.3 74.4 1.0
SG A:CYS19 2.5 49.8 1.0
CE1 A:HIS33 2.7 35.3 1.0
CD2 A:HIS33 2.9 35.7 1.0
CG A:HIS39 3.0 69.2 1.0
CE1 A:HIS39 3.1 66.8 1.0
N A:CYS19 3.3 52.9 1.0
CB A:HIS39 3.3 61.7 1.0
CB A:CYS16 3.4 73.3 1.0
CB A:CYS19 3.5 41.2 1.0
CA A:CYS19 3.8 50.2 1.0
ND1 A:HIS33 3.9 37.5 1.0
CG A:HIS33 4.0 37.1 1.0
CD2 A:HIS39 4.2 70.0 1.0
NE2 A:HIS39 4.2 67.3 1.0
C A:ALA18 4.3 58.8 1.0
CB A:ALA18 4.4 64.1 1.0
CB A:ALA110 4.4 54.1 1.0
CA A:ALA18 4.7 63.7 1.0
CA A:CYS16 4.8 68.5 1.0
CE2 A:PHE106 4.8 43.0 1.0
CZ A:PHE106 4.8 43.9 1.0
CA A:HIS39 4.8 59.5 1.0
N A:ALA18 4.8 51.6 1.0

Zinc binding site 3 out of 6 in 5rm7

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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 Z69118333


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 Z69118333 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:92.0
occ:1.00
 SG A:CYS5 2.0 64.3 1.0
SG A:CYS29 2.4 87.6 1.0
SG A:CYS8 2.4 0.0 1.0
SG A:CYS26 2.6 86.2 1.0
CB A:CYS29 3.0 88.6 1.0
CB A:CYS5 3.4 77.1 1.0
CB A:CYS8 3.5 99.0 1.0
CB A:CYS26 3.5 76.9 1.0
N A:CYS8 3.7 98.6 1.0
N A:CYS26 4.0 71.2 1.0
CB A:LEU7 4.1 91.8 1.0
CA A:CYS8 4.1 97.5 1.0
CA A:CYS26 4.3 78.1 1.0
CA A:CYS29 4.3 85.2 1.0
N A:CYS29 4.4 84.7 1.0
C A:LEU7 4.5 93.2 1.0
CA A:LEU7 4.7 88.0 1.0
C A:CYS8 4.7 90.8 1.0
CA A:CYS5 4.7 83.0 1.0
O A:CYS26 4.7 93.6 1.0
N A:LEU7 4.8 77.2 1.0
C A:CYS26 4.9 85.9 1.0
O A:CYS5 5.0 77.4 1.0
N A:ASN9 5.0 92.1 1.0

Zinc binding site 4 out of 6 in 5rm7

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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 Z69118333


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 Z69118333 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:37.0
occ:1.00
 NE2 B:HIS33 2.0 35.8 1.0
ND1 B:HIS39 2.0 38.9 1.0
SG B:CYS16 2.1 38.1 1.0
SG B:CYS19 2.4 40.9 1.0
CD2 B:HIS33 2.9 33.6 1.0
CG B:HIS39 3.0 44.5 1.0
CE1 B:HIS39 3.0 41.7 1.0
CE1 B:HIS33 3.1 38.0 1.0
CB B:CYS16 3.3 41.1 1.0
CB B:HIS39 3.3 42.1 1.0
CB B:CYS19 3.4 36.4 1.0
N B:CYS19 3.5 43.0 1.0
CA B:CYS19 3.8 41.4 1.0
CG B:HIS33 4.1 35.9 1.0
ND1 B:HIS33 4.1 34.1 1.0
CD2 B:HIS39 4.2 45.2 1.0
NE2 B:HIS39 4.2 44.8 1.0
C B:ALA18 4.3 42.7 1.0
CB B:ALA18 4.4 37.3 1.0
CB B:ALA110 4.6 36.9 1.0
CA B:CYS16 4.6 40.0 1.0
CA B:ALA18 4.8 40.6 1.0
CA B:HIS39 4.8 43.3 1.0
N B:ALA18 4.8 39.2 1.0
C B:CYS16 5.0 43.3 1.0

Zinc binding site 5 out of 6 in 5rm7

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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 Z69118333


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 Z69118333 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:53.4
occ:1.00
 SG B:CYS29 2.2 52.2 1.0
SG B:CYS26 2.4 48.4 1.0
SG B:CYS5 2.4 52.2 1.0
CB B:CYS8 2.8 63.4 1.0
SG B:CYS8 2.8 87.7 1.0
CB B:CYS29 2.9 44.0 1.0
CB B:CYS5 3.5 58.5 1.0
CB B:CYS26 3.8 52.8 1.0
N B:CYS8 3.9 69.5 1.0
CA B:CYS8 3.9 70.4 1.0
N B:CYS29 4.0 42.6 1.0
CA B:CYS29 4.1 42.1 1.0
N B:CYS26 4.1 55.5 1.0
CB B:LEU7 4.5 71.8 1.0
CA B:CYS26 4.5 53.6 1.0
C B:LEU7 4.6 70.0 1.0
CA B:GLY99 4.6 65.1 1.0
N B:GLY99 4.6 67.1 1.0
OG B:SER10 4.9 58.3 1.0
CB B:SER10 4.9 59.7 1.0
CA B:CYS5 4.9 61.1 1.0
OG B:SER100 4.9 68.5 1.0
CA B:LEU7 4.9 69.3 1.0
N B:LEU7 5.0 60.6 1.0
C B:GLY99 5.0 61.4 1.0
O B:GLY99 5.0 64.5 1.0
O B:CYS26 5.0 47.4 1.0

Zinc binding site 6 out of 6 in 5rm7

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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 Z69118333


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 Z69118333 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:61.8
occ:1.00
 SG B:CYS50 2.3 54.1 1.0
ND1 B:HIS75 2.3 78.8 1.0
SG B:CYS55 2.4 67.9 1.0
SG B:CYS72 2.6 54.4 1.0
CB B:CYS50 3.1 59.0 1.0
CB B:CYS55 3.2 74.0 1.0
CG B:HIS75 3.2 77.3 1.0
CE1 B:HIS75 3.4 75.1 1.0
CB B:HIS75 3.4 68.8 1.0
CB B:CYS72 3.5 54.9 1.0
N B:CYS72 3.8 52.6 1.0
CB B:ALA52 4.0 73.8 1.0
CA B:CYS72 4.2 57.6 1.0
CD2 B:HIS75 4.4 82.3 1.0
N B:HIS75 4.5 57.3 1.0
NE2 B:HIS75 4.5 82.4 1.0
CA B:CYS50 4.5 61.4 1.0
CG2 B:VAL57 4.5 71.3 1.0
CA B:HIS75 4.6 63.9 1.0
CA B:CYS55 4.7 76.5 1.0
CB B:VAL57 4.7 76.1 1.0
C B:CYS72 4.9 62.9 1.0
C B:TYR71 5.0 55.7 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 04:17:42 2024

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