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Zinc in PDB 5rlp: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z166605480

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z166605480

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z166605480:
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 Z166605480, PDB code: 5rlp 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) 81.65 / 2.56
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.200, 70.258, 85.676, 102.75, 96.19, 112.40
R / Rfree (%) 14.1 / 25.3

Other elements in 5rlp:

The structure of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z166605480 also contains other interesting chemical elements:

Fluorine (F) 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 Z166605480 (pdb code 5rlp). 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 Z166605480, PDB code: 5rlp:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlp

Go back to Zinc Binding Sites List in 5rlp
Zinc binding site 1 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z166605480


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 Z166605480 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:79.4
occ:1.00
 SG A:CYS55 2.3 91.6 1.0
ND1 A:HIS75 2.3 71.4 1.0
SG A:CYS50 2.4 70.4 1.0
SG A:CYS72 2.9 84.5 1.0
CB A:CYS55 3.3 93.5 1.0
CG A:HIS75 3.3 70.4 1.0
CE1 A:HIS75 3.3 68.8 1.0
CB A:CYS50 3.4 79.4 1.0
CB A:CYS72 3.4 83.2 1.0
CB A:HIS75 3.5 69.8 1.0
N A:CYS72 3.9 75.3 1.0
CB A:ALA52 4.1 75.0 1.0
CA A:CYS72 4.2 80.7 1.0
CG2 A:VAL57 4.3 82.7 1.0
N A:HIS75 4.4 73.4 1.0
CD2 A:HIS75 4.4 67.5 1.0
NE2 A:HIS75 4.5 65.6 1.0
CA A:HIS75 4.6 73.3 1.0
CB A:VAL57 4.6 84.7 1.0
CA A:CYS55 4.7 95.3 1.0
CA A:CYS50 4.8 82.0 1.0
C A:CYS72 5.0 80.9 1.0

Zinc binding site 2 out of 6 in 5rlp

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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 Z166605480


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 Z166605480 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:82.0
occ:1.00
 NE2 A:HIS33 2.0 73.5 1.0
SG A:CYS16 2.3 0.9 1.0
SG A:CYS19 2.4 93.7 1.0
ND1 A:HIS39 2.6 0.9 1.0
CE1 A:HIS33 2.8 74.0 1.0
CD2 A:HIS33 3.1 75.8 1.0
CG A:HIS39 3.2 0.9 1.0
CB A:CYS16 3.3 99.5 1.0
CB A:CYS19 3.4 85.3 1.0
CE1 A:HIS39 3.4 0.1 1.0
CB A:HIS39 3.5 0.1 1.0
N A:CYS19 3.6 87.1 1.0
CA A:CYS19 3.8 89.6 1.0
ND1 A:HIS33 4.0 74.9 1.0
CG A:HIS33 4.2 76.5 1.0
CD2 A:HIS39 4.2 0.5 1.0
C A:ALA18 4.3 92.8 1.0
CB A:ALA110 4.3 74.0 1.0
NE2 A:HIS39 4.3 0.1 1.0
CB A:ALA18 4.6 95.5 1.0
CA A:CYS16 4.7 0.9 1.0
CE2 A:PHE106 4.8 99.4 1.0
CA A:ALA18 4.9 93.4 1.0
O A:ALA18 4.9 91.3 1.0
CZ A:PHE106 5.0 0.2 1.0
CA A:HIS39 5.0 94.7 1.0

Zinc binding site 3 out of 6 in 5rlp

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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 Z166605480


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 Z166605480 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:0.7
occ:1.00
 SG A:CYS5 2.2 0.4 1.0
SG A:CYS26 2.6 0.7 1.0
SG A:CYS8 2.6 0.3 1.0
SG A:CYS29 2.9 0.1 1.0
CB A:CYS26 3.2 0.5 1.0
CB A:CYS5 3.2 0.7 1.0
N A:CYS8 3.3 0.2 1.0
CB A:CYS29 3.4 1.0 1.0
CB A:CYS8 3.5 0.4 1.0
CA A:CYS8 3.7 0.1 1.0
N A:CYS26 3.8 0.6 1.0
CA A:CYS26 4.0 0.8 1.0
C A:CYS8 4.2 0.9 1.0
CB A:LEU7 4.2 0.5 1.0
C A:LEU7 4.3 0.7 1.0
N A:ASN9 4.4 0.6 1.0
CA A:CYS5 4.6 0.5 1.0
CA A:LEU7 4.6 0.5 1.0
N A:LEU7 4.6 0.2 1.0
OG A:SER10 4.7 0.5 1.0
N A:SER10 4.7 1.0 1.0
CA A:CYS29 4.7 0.1 1.0
CB A:SER10 4.7 0.6 1.0
N A:CYS29 4.8 0.8 1.0
C A:CYS26 4.8 0.5 1.0
O A:CYS26 4.8 0.0 1.0
O A:CYS8 4.9 0.1 1.0
C A:CYS5 4.9 0.4 1.0

Zinc binding site 4 out of 6 in 5rlp

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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 Z166605480


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 Z166605480 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:60.9
occ:1.00
 NE2 B:HIS33 2.0 60.6 1.0
SG B:CYS16 2.3 69.6 1.0
ND1 B:HIS39 2.4 73.8 1.0
SG B:CYS19 2.6 60.4 1.0
CE1 B:HIS33 2.9 59.6 1.0
CG B:HIS39 3.0 71.8 1.0
CD2 B:HIS33 3.2 60.8 1.0
CB B:HIS39 3.3 71.0 1.0
CE1 B:HIS39 3.3 72.7 1.0
CB B:CYS16 3.4 72.6 1.0
CB B:CYS19 3.5 64.5 1.0
N B:CYS19 3.5 66.0 1.0
CA B:CYS19 3.8 67.1 1.0
CD2 B:HIS39 4.1 71.5 1.0
ND1 B:HIS33 4.1 60.6 1.0
NE2 B:HIS39 4.2 73.0 1.0
C B:ALA18 4.2 66.8 1.0
CG B:HIS33 4.2 62.0 1.0
CB B:ALA18 4.5 62.6 1.0
CB B:ALA110 4.5 57.8 1.0
CA B:ALA18 4.7 66.6 1.0
CA B:CYS16 4.8 71.4 1.0
CA B:HIS39 4.8 69.7 1.0
O B:ALA18 4.9 71.2 1.0
N B:ALA18 4.9 68.7 1.0

Zinc binding site 5 out of 6 in 5rlp

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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 Z166605480


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 Z166605480 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:92.2
occ:1.00
 SG B:CYS26 2.2 70.4 1.0
SG B:CYS5 2.2 87.0 1.0
CB B:CYS8 2.7 98.5 1.0
SG B:CYS29 2.7 76.6 1.0
CB B:CYS29 3.2 72.2 1.0
CB B:CYS5 3.2 90.2 1.0
N B:CYS8 3.4 96.0 1.0
CB B:CYS26 3.5 74.3 1.0
CA B:CYS8 3.6 97.6 1.0
SG B:CYS8 3.8 0.6 1.0
N B:CYS26 3.8 74.6 1.0
CA B:CYS26 4.2 75.1 1.0
C B:LEU7 4.3 93.3 1.0
N B:CYS29 4.3 73.7 1.0
CA B:CYS29 4.4 70.5 1.0
CB B:LEU7 4.4 92.0 1.0
C B:CYS8 4.5 99.2 1.0
OG B:SER10 4.5 85.0 1.0
N B:ASN9 4.6 99.0 1.0
CA B:CYS5 4.7 88.9 1.0
CB B:SER10 4.7 89.2 1.0
CA B:LEU7 4.7 90.7 1.0
N B:LEU7 4.8 90.3 1.0
N B:GLY99 4.8 1.0 1.0
N B:SER10 4.8 92.3 1.0
CA B:GLY99 4.9 0.7 1.0
C B:CYS26 5.0 77.0 1.0
C B:LEU25 5.0 73.4 1.0

Zinc binding site 6 out of 6 in 5rlp

Go back to Zinc Binding Sites List in 5rlp
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z166605480


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 Z166605480 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:98.2
occ:1.00
 SG B:CYS50 2.2 96.4 1.0
SG B:CYS55 2.4 0.6 1.0
ND1 B:HIS75 2.4 0.9 1.0
SG B:CYS72 3.1 0.7 1.0
CB B:CYS55 3.2 0.6 1.0
CB B:CYS50 3.2 0.6 1.0
CG B:HIS75 3.3 0.6 1.0
CE1 B:HIS75 3.4 98.7 1.0
CB B:HIS75 3.5 0.0 1.0
CB B:CYS72 3.5 0.4 1.0
N B:CYS72 3.8 95.3 1.0
CB B:ALA52 3.9 0.2 1.0
CA B:CYS72 4.2 0.5 1.0
CG2 B:VAL57 4.4 98.9 1.0
N B:HIS75 4.4 0.6 1.0
CD2 B:HIS75 4.5 0.3 1.0
NE2 B:HIS75 4.5 0.6 1.0
CA B:HIS75 4.6 1.0 1.0
CA B:CYS50 4.6 0.4 1.0
CB B:VAL57 4.6 0.8 1.0
CA B:CYS55 4.7 0.7 1.0
C B:TYR71 4.9 93.3 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 04:06:32 2024

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