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Zinc in PDB 5rmm: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with POB0066

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with POB0066

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with POB0066:
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 POB0066, PDB code: 5rmm 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) 81.56 / 2.20
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.009, 70.028, 85.753, 103.16, 96.14, 112.25
R / Rfree (%) 16.8 / 25.5

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 POB0066 (pdb code 5rmm). 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 POB0066, PDB code: 5rmm:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rmm

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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 POB0066


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 POB0066 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:71.6
occ:1.00
 ND1 A:HIS75 2.1 63.9 1.0
SG A:CYS55 2.3 78.8 1.0
SG A:CYS50 2.4 65.3 1.0
SG A:CYS72 2.7 71.1 1.0
CE1 A:HIS75 3.1 63.7 1.0
CG A:HIS75 3.2 64.5 1.0
CB A:CYS50 3.3 70.5 1.0
CB A:CYS55 3.3 73.2 1.0
CB A:CYS72 3.4 72.5 1.0
CB A:HIS75 3.6 65.0 1.0
N A:CYS72 3.8 68.5 1.0
CA A:CYS72 4.2 70.4 1.0
NE2 A:HIS75 4.3 60.2 1.0
CB A:ALA52 4.3 61.1 1.0
CD2 A:HIS75 4.3 61.2 1.0
CG2 A:VAL57 4.5 73.3 1.0
N A:HIS75 4.6 68.6 1.0
CB A:VAL57 4.6 72.9 1.0
CA A:HIS75 4.7 65.5 1.0
CA A:CYS55 4.7 74.2 1.0
CA A:CYS50 4.8 72.6 1.0
C A:TYR71 4.9 65.8 1.0
C A:CYS72 4.9 72.6 1.0

Zinc binding site 2 out of 6 in 5rmm

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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 POB0066


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 POB0066 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:70.7
occ:1.00
 ND1 A:HIS39 2.1 74.2 1.0
NE2 A:HIS33 2.1 69.7 1.0
SG A:CYS16 2.2 87.7 1.0
SG A:CYS19 2.3 73.3 1.0
CE1 A:HIS33 3.0 71.4 1.0
CE1 A:HIS39 3.0 74.8 1.0
CG A:HIS39 3.1 76.8 1.0
CD2 A:HIS33 3.2 72.6 1.0
CB A:CYS16 3.3 86.7 1.0
CB A:CYS19 3.4 75.6 1.0
N A:CYS19 3.4 73.8 1.0
CB A:HIS39 3.4 75.9 1.0
CA A:CYS19 3.7 76.1 1.0
C A:ALA18 4.1 76.8 1.0
ND1 A:HIS33 4.2 72.9 1.0
NE2 A:HIS39 4.2 79.6 1.0
CD2 A:HIS39 4.2 79.3 1.0
CG A:HIS33 4.2 74.0 1.0
CB A:ALA110 4.4 60.6 1.0
CB A:ALA18 4.4 77.3 1.0
CA A:ALA18 4.6 78.3 1.0
CA A:CYS16 4.6 85.8 1.0
N A:ALA18 4.7 77.3 1.0
O A:ALA18 4.8 75.5 1.0
CA A:HIS39 4.9 76.5 1.0
CE2 A:PHE106 4.9 73.3 1.0
C A:CYS16 4.9 81.8 1.0

Zinc binding site 3 out of 6 in 5rmm

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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 POB0066


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 POB0066 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.5
occ:1.00
 SG A:CYS29 2.3 0.9 1.0
SG A:CYS8 2.4 0.0 1.0
SG A:CYS5 2.5 92.7 1.0
SG A:CYS26 2.7 0.1 1.0
CB A:CYS29 3.1 95.2 1.0
CB A:CYS26 3.1 0.9 1.0
CB A:CYS8 3.3 0.3 1.0
N A:CYS8 3.6 0.8 1.0
CB A:CYS5 3.7 0.7 1.0
N A:CYS26 3.8 0.1 1.0
CA A:CYS8 4.0 0.4 1.0
CA A:CYS26 4.0 0.3 1.0
CB A:LEU7 4.1 0.6 1.0
CA A:CYS29 4.3 93.8 1.0
C A:LEU7 4.4 0.9 1.0
N A:CYS29 4.4 96.4 1.0
CA A:LEU7 4.7 0.7 1.0
C A:CYS8 4.7 0.7 1.0
C A:CYS26 4.8 0.6 1.0
N A:LEU7 4.8 0.5 1.0
OG A:SER10 4.9 0.5 1.0

Zinc binding site 4 out of 6 in 5rmm

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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 POB0066


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 POB0066 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:54.6
occ:1.00
 ND1 B:HIS39 2.0 63.2 1.0
NE2 B:HIS33 2.0 54.2 1.0
SG B:CYS16 2.3 56.4 1.0
SG B:CYS19 2.5 58.6 1.0
CE1 B:HIS33 2.9 52.6 1.0
CG B:HIS39 3.0 63.5 1.0
CE1 B:HIS39 3.0 62.2 1.0
CD2 B:HIS33 3.1 53.6 1.0
CB B:HIS39 3.3 64.4 1.0
CB B:CYS16 3.4 59.0 1.0
CB B:CYS19 3.4 60.4 1.0
N B:CYS19 3.5 63.3 1.0
CA B:CYS19 3.7 62.8 1.0
ND1 B:HIS33 4.1 51.6 1.0
C B:ALA18 4.1 63.2 1.0
CD2 B:HIS39 4.1 61.3 1.0
NE2 B:HIS39 4.1 60.0 1.0
CG B:HIS33 4.2 53.1 1.0
CB B:ALA18 4.4 59.8 1.0
CB B:ALA110 4.4 51.5 1.0
CA B:ALA18 4.6 62.0 1.0
CA B:CYS16 4.8 58.7 1.0
CA B:HIS39 4.8 63.5 1.0
N B:ALA18 4.8 63.7 1.0
O B:ALA18 4.8 64.0 1.0

Zinc binding site 5 out of 6 in 5rmm

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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 POB0066


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 POB0066 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:80.9
occ:1.00
 SG B:CYS26 2.2 70.9 1.0
SG B:CYS5 2.4 79.2 1.0
SG B:CYS29 2.5 68.9 1.0
CB B:CYS8 3.0 0.3 1.0
CB B:CYS29 3.3 63.8 1.0
CB B:CYS5 3.4 82.9 1.0
N B:CYS8 3.5 93.2 1.0
CB B:CYS26 3.5 66.8 1.0
CA B:CYS8 3.7 98.0 1.0
N B:CYS26 4.0 64.8 1.0
N B:GLY99 4.2 95.1 1.0
SG B:CYS8 4.2 0.5 1.0
N B:CYS29 4.3 63.0 1.0
CA B:CYS26 4.3 64.1 1.0
C B:CYS8 4.4 96.9 1.0
CA B:CYS29 4.4 62.3 1.0
C B:LEU7 4.4 89.6 1.0
OG B:SER10 4.4 93.7 1.0
CB B:LEU7 4.5 83.2 1.0
CA B:GLY99 4.5 93.8 1.0
CB B:SER10 4.6 91.7 1.0
N B:ASN9 4.7 97.0 1.0
N B:SER10 4.8 92.2 1.0
CA B:CYS5 4.8 80.1 1.0
CA B:LEU7 4.8 84.0 1.0
OG B:SER100 4.9 0.8 1.0
N B:LEU7 4.9 80.6 1.0
O B:CYS8 5.0 95.6 1.0

Zinc binding site 6 out of 6 in 5rmm

Go back to Zinc Binding Sites List in 5rmm
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with POB0066


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 POB0066 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:94.7
occ:1.00
 SG B:CYS50 2.3 87.3 1.0
ND1 B:HIS75 2.4 93.6 1.0
SG B:CYS55 2.5 0.6 1.0
SG B:CYS72 2.7 93.4 1.0
CB B:CYS55 3.2 0.3 1.0
CG B:HIS75 3.2 94.1 1.0
CB B:CYS50 3.3 93.3 1.0
CB B:HIS75 3.3 91.6 1.0
CB B:CYS72 3.4 88.9 1.0
CE1 B:HIS75 3.4 97.1 1.0
N B:CYS72 3.7 87.5 1.0
CA B:CYS72 4.1 90.8 1.0
CB B:ALA52 4.1 0.9 1.0
N B:HIS75 4.3 92.8 1.0
CD2 B:HIS75 4.4 97.5 1.0
CA B:HIS75 4.5 93.7 1.0
NE2 B:HIS75 4.5 0.1 1.0
CG2 B:VAL57 4.6 0.1 1.0
CA B:CYS55 4.6 0.1 1.0
CB B:VAL57 4.7 0.2 1.0
CA B:CYS50 4.7 93.1 1.0
C B:CYS72 4.7 92.5 1.0
C B:SER74 4.8 95.7 1.0
C B:TYR71 4.9 88.0 1.0
O B:CYS72 4.9 88.5 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 04:29:04 2024

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