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Zinc in PDB 5rob: Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase

Enzymatic activity of Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase

All present enzymatic activity of Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase:
3.6.4.12; 3.6.4.13;

Protein crystallography data

The structure of Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase, PDB code: 5rob 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) 80.92 / 1.87
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.242, 70.282, 84.616, 102.4, 95.71, 112.84
R / Rfree (%) 21.9 / 25.4

Zinc Binding Sites:

The binding sites of Zinc atom in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase (pdb code 5rob). 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 of Ground-State Model of Sars-Cov-2 Helicase, PDB code: 5rob:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rob

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Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase


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 of Ground-State Model of Sars-Cov-2 Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:37.9
occ:1.00
 NE2 B:HIS33 2.1 30.6 1.0
SG B:CYS16 2.1 40.8 1.0
ND1 B:HIS39 2.1 40.7 1.0
SG B:CYS19 2.4 38.3 1.0
CD2 B:HIS33 3.0 30.2 1.0
CG B:HIS39 3.1 43.3 1.0
CB B:CYS16 3.1 46.9 1.0
CE1 B:HIS39 3.1 44.1 1.0
CE1 B:HIS33 3.2 33.7 1.0
CB B:CYS19 3.3 35.5 1.0
CB B:HIS39 3.3 39.9 1.0
N B:CYS19 3.4 46.5 1.0
CA B:CYS19 3.7 41.4 1.0
CG B:HIS33 4.2 34.5 1.0
CD2 B:HIS39 4.2 44.3 1.0
NE2 B:HIS39 4.2 41.2 1.0
ND1 B:HIS33 4.2 30.3 1.0
C B:ALA18 4.4 47.8 1.0
CB B:ALA110 4.5 38.7 1.0
CA B:CYS16 4.5 47.9 1.0
O B:CYS16 4.6 52.0 1.0
CB B:ALA18 4.7 45.8 1.0
C B:CYS16 4.7 42.7 1.0
CA B:HIS39 4.8 38.9 1.0
N B:ALA18 4.8 43.5 1.0
CE2 B:PHE106 4.8 30.4 1.0
CA B:ALA18 4.9 47.5 1.0
CZ B:PHE106 5.0 38.2 1.0

Zinc binding site 2 out of 6 in 5rob

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Zinc binding site 2 out of 6 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase


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 of Ground-State Model of Sars-Cov-2 Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:52.9
occ:1.00
 SG B:CYS26 2.3 53.0 1.0
SG B:CYS29 2.3 55.8 1.0
SG B:CYS5 2.4 55.0 1.0
SG B:CYS8 2.7 64.5 1.0
CB B:CYS29 2.9 56.9 1.0
CB B:CYS8 3.1 65.2 1.0
CB B:CYS26 3.2 55.5 1.0
CB B:CYS5 3.5 62.3 1.0
N B:CYS8 3.8 63.9 1.0
CA B:GLY99 3.9 55.5 1.0
N B:CYS26 4.0 51.9 1.0
CA B:CYS8 4.0 67.9 1.0
N B:CYS29 4.0 52.7 1.0
N B:GLY99 4.1 57.8 1.0
CA B:CYS29 4.1 54.5 1.0
CA B:CYS26 4.1 54.3 1.0
CB B:LEU7 4.3 67.3 1.0
C B:GLY99 4.5 53.9 1.0
C B:LEU7 4.5 58.8 1.0
O B:CYS26 4.7 43.9 1.0
C B:CYS26 4.7 53.1 1.0
OG B:SER100 4.7 58.0 1.0
O B:GLY99 4.8 48.9 1.0
CA B:LEU7 4.9 64.1 1.0
CA B:CYS5 4.9 61.8 1.0
CB B:SER10 5.0 60.7 1.0

Zinc binding site 3 out of 6 in 5rob

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Zinc binding site 3 out of 6 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase


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 of Ground-State Model of Sars-Cov-2 Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:65.0
occ:1.00
 SG B:CYS50 2.3 61.1 1.0
ND1 B:HIS75 2.3 57.4 1.0
SG B:CYS55 2.3 75.6 1.0
SG B:CYS72 2.6 51.4 1.0
CB B:CYS55 3.2 81.4 1.0
CG B:HIS75 3.2 56.6 1.0
CE1 B:HIS75 3.2 62.7 1.0
CB B:CYS50 3.4 58.2 1.0
CB B:CYS72 3.4 52.6 1.0
CB B:HIS75 3.5 56.3 1.0
CB B:ALA52 3.7 75.9 1.0
N B:CYS72 3.9 48.3 1.0
CA B:CYS72 4.2 52.3 1.0
CD2 B:HIS75 4.4 60.3 1.0
NE2 B:HIS75 4.4 58.6 1.0
N B:HIS75 4.6 58.9 1.0
CA B:HIS75 4.6 60.9 1.0
CA B:CYS55 4.6 79.3 1.0
CG2 B:VAL57 4.7 61.2 1.0
CA B:CYS50 4.8 56.1 1.0
CB B:VAL57 4.8 64.9 1.0
C B:CYS72 4.9 56.0 1.0
CA B:ALA52 5.0 76.5 1.0
C B:TYR71 5.0 49.4 1.0

Zinc binding site 4 out of 6 in 5rob

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Zinc binding site 4 out of 6 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase


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 of Ground-State Model of Sars-Cov-2 Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:48.2
occ:1.00
 ND1 A:HIS75 2.2 36.6 1.0
SG A:CYS55 2.2 44.9 1.0
SG A:CYS50 2.3 43.7 1.0
SG A:CYS72 2.5 45.5 1.0
CE1 A:HIS75 3.0 38.8 1.0
CB A:CYS50 3.1 44.5 1.0
CG A:HIS75 3.2 35.8 1.0
CB A:CYS55 3.3 50.8 1.0
CB A:CYS72 3.3 44.3 1.0
CB A:HIS75 3.6 39.8 1.0
N A:CYS72 3.8 40.7 1.0
CA A:CYS72 4.1 44.4 1.0
CB A:ALA52 4.2 45.9 1.0
NE2 A:HIS75 4.2 34.6 1.0
CD2 A:HIS75 4.3 35.8 1.0
N A:HIS75 4.5 42.0 1.0
CG2 A:VAL57 4.5 49.0 1.0
CA A:CYS50 4.6 43.4 1.0
CA A:CYS55 4.7 51.1 1.0
CB A:VAL57 4.7 46.9 1.0
CA A:HIS75 4.8 41.2 1.0
C A:CYS72 4.8 47.5 1.0
C A:TYR71 5.0 37.2 1.0
O A:CYS72 5.0 46.5 1.0

Zinc binding site 5 out of 6 in 5rob

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Zinc binding site 5 out of 6 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase


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 of Ground-State Model of Sars-Cov-2 Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:39.6
occ:1.00
 NE2 A:HIS33 1.9 26.3 1.0
ND1 A:HIS39 2.1 36.0 1.0
SG A:CYS16 2.2 44.3 1.0
SG A:CYS19 2.5 45.7 1.0
CD2 A:HIS33 2.9 33.4 1.0
CE1 A:HIS33 2.9 31.9 1.0
CE1 A:HIS39 3.0 42.8 1.0
CG A:HIS39 3.1 42.4 1.0
CB A:CYS16 3.2 44.7 1.0
N A:CYS19 3.3 45.4 1.0
CB A:HIS39 3.4 39.2 1.0
CB A:CYS19 3.6 41.6 1.0
CA A:CYS19 3.8 43.7 1.0
ND1 A:HIS33 4.0 30.5 1.0
CG A:HIS33 4.0 33.5 1.0
NE2 A:HIS39 4.1 44.2 1.0
CD2 A:HIS39 4.2 43.2 1.0
C A:ALA18 4.2 44.9 1.0
CB A:ALA18 4.2 45.6 1.0
CB A:ALA110 4.5 45.5 1.0
CA A:CYS16 4.6 43.4 1.0
CA A:ALA18 4.6 44.8 1.0
N A:ALA18 4.7 44.6 1.0
CA A:HIS39 4.9 43.2 1.0
CE2 A:PHE106 4.9 39.9 1.0
C A:CYS16 4.9 42.8 1.0
CZ A:PHE106 5.0 38.4 1.0

Zinc binding site 6 out of 6 in 5rob

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Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition of Ground-State Model of Sars-Cov-2 Helicase


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 of Ground-State Model of Sars-Cov-2 Helicase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:57.6
occ:1.00
 SG A:CYS5 2.2 63.0 1.0
SG A:CYS26 2.3 63.2 1.0
SG A:CYS29 2.3 55.1 1.0
SG A:CYS8 2.5 69.0 1.0
CB A:CYS29 3.0 57.7 1.0
CB A:CYS26 3.1 55.5 1.0
CB A:CYS5 3.2 58.8 1.0
CB A:CYS8 3.3 63.6 1.0
N A:CYS26 3.6 51.8 1.0
N A:CYS8 3.9 63.0 1.0
CA A:CYS26 3.9 55.1 1.0
CA A:CYS8 4.2 64.8 1.0
CA A:CYS29 4.2 55.6 1.0
N A:CYS29 4.2 57.6 1.0
CB A:LEU7 4.4 68.2 1.0
C A:CYS26 4.6 55.4 1.0
O A:CYS26 4.6 57.0 1.0
CA A:CYS5 4.6 63.0 1.0
C A:LEU7 4.7 63.2 1.0
C A:LEU25 4.8 50.7 1.0
C A:CYS8 4.8 63.4 1.0
CA A:LEU7 4.9 64.8 1.0
N A:LEU7 4.9 62.9 1.0
OG A:SER10 4.9 57.4 1.0
CB A:SER10 5.0 63.4 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 of Ground-State Model To Be Published.
Page generated: Mon Oct 28 04:29:04 2024

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