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Zinc in PDB 5rlf: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z235341991

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z235341991

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z235341991:
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 Z235341991, PDB code: 5rlf 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) 81.93 / 2.24
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.270, 70.425, 86.158, 102.99, 96.42, 112.18
R / Rfree (%) 16.1 / 25.4

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 Z235341991 (pdb code 5rlf). 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 Z235341991, PDB code: 5rlf:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rlf

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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 Z235341991


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 Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:77.7
occ:1.00
 ND1 A:HIS75 2.3 75.0 1.0
SG A:CYS50 2.3 76.7 1.0
SG A:CYS55 2.4 87.8 1.0
SG A:CYS72 2.9 76.0 1.0
CE1 A:HIS75 3.3 74.0 1.0
CG A:HIS75 3.3 74.3 1.0
CB A:CYS50 3.3 79.7 1.0
CB A:CYS55 3.3 89.3 1.0
CB A:CYS72 3.4 77.3 1.0
CB A:HIS75 3.6 73.4 1.0
N A:CYS72 3.8 72.3 1.0
CA A:CYS72 4.1 75.7 1.0
CB A:ALA52 4.2 69.2 1.0
NE2 A:HIS75 4.4 70.1 1.0
CD2 A:HIS75 4.4 71.5 1.0
N A:HIS75 4.5 77.8 1.0
CG2 A:VAL57 4.5 80.2 1.0
CA A:HIS75 4.7 75.6 1.0
CB A:VAL57 4.7 81.7 1.0
CA A:CYS50 4.7 79.7 1.0
CA A:CYS55 4.8 91.3 1.0
C A:TYR71 4.9 69.7 1.0
C A:CYS72 4.9 80.3 1.0

Zinc binding site 2 out of 6 in 5rlf

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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 Z235341991


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 Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:75.6
occ:1.00
 NE2 A:HIS33 2.0 72.6 1.0
ND1 A:HIS39 2.0 86.5 1.0
SG A:CYS16 2.3 96.2 1.0
SG A:CYS19 2.3 80.8 1.0
CE1 A:HIS33 3.0 73.7 1.0
CD2 A:HIS33 3.0 76.8 1.0
CE1 A:HIS39 3.0 88.6 1.0
CG A:HIS39 3.1 87.6 1.0
CB A:HIS39 3.4 84.4 1.0
CB A:CYS19 3.4 74.8 1.0
N A:CYS19 3.4 77.0 1.0
CB A:CYS16 3.4 99.9 1.0
CA A:CYS19 3.7 79.9 1.0
C A:ALA18 4.1 79.3 1.0
ND1 A:HIS33 4.1 75.6 1.0
CG A:HIS33 4.2 78.3 1.0
NE2 A:HIS39 4.2 89.7 1.0
CD2 A:HIS39 4.2 89.0 1.0
CB A:ALA110 4.4 74.8 1.0
CB A:ALA18 4.4 81.1 1.0
CA A:ALA18 4.6 81.3 1.0
N A:ALA18 4.8 81.7 1.0
CA A:CYS16 4.8 99.6 1.0
O A:ALA18 4.8 78.9 1.0
CA A:HIS39 4.9 83.8 1.0
CE2 A:PHE106 5.0 89.0 1.0

Zinc binding site 3 out of 6 in 5rlf

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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 Z235341991


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 Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn704

b:0.4
occ:1.00
 SG A:CYS5 2.2 0.2 1.0
SG A:CYS29 2.5 0.9 1.0
SG A:CYS26 2.5 0.6 1.0
SG A:CYS8 2.5 0.1 1.0
CB A:CYS29 3.1 0.0 1.0
CB A:CYS26 3.3 0.3 1.0
N A:CYS8 3.6 0.1 1.0
CB A:CYS8 3.6 0.4 1.0
CB A:CYS5 3.6 0.8 1.0
N A:CYS26 3.8 0.5 1.0
CA A:CYS8 4.0 0.8 1.0
CA A:CYS26 4.1 1.0 1.0
CB A:LEU7 4.3 0.7 1.0
CA A:CYS29 4.3 0.9 1.0
N A:CYS29 4.3 0.2 1.0
C A:LEU7 4.6 0.0 1.0
C A:CYS8 4.6 0.2 1.0
N A:ASN9 4.7 0.5 1.0
CA A:LEU7 4.8 0.0 1.0
OG A:SER10 4.9 0.3 1.0
CA A:CYS5 4.9 0.5 1.0
C A:LEU25 4.9 1.0 1.0
C A:CYS26 4.9 0.3 1.0
CB A:SER10 5.0 0.6 1.0
N A:SER10 5.0 0.9 1.0

Zinc binding site 4 out of 6 in 5rlf

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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 Z235341991


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 Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn701

b:62.4
occ:1.00
 NE2 B:HIS33 2.0 61.0 1.0
ND1 B:HIS39 2.1 67.2 1.0
SG B:CYS16 2.2 70.2 1.0
SG B:CYS19 2.5 59.0 1.0
CD2 B:HIS33 2.9 61.1 1.0
CE1 B:HIS33 3.0 60.0 1.0
CG B:HIS39 3.0 69.6 1.0
CE1 B:HIS39 3.1 66.8 1.0
CB B:HIS39 3.3 72.1 1.0
CB B:CYS16 3.4 67.5 1.0
N B:CYS19 3.4 64.9 1.0
CB B:CYS19 3.4 61.8 1.0
CA B:CYS19 3.8 63.4 1.0
CG B:HIS33 4.1 61.4 1.0
ND1 B:HIS33 4.1 60.1 1.0
C B:ALA18 4.1 64.0 1.0
CD2 B:HIS39 4.2 68.5 1.0
NE2 B:HIS39 4.2 66.2 1.0
CB B:ALA18 4.4 59.3 1.0
CB B:ALA110 4.5 55.7 1.0
CA B:ALA18 4.6 62.4 1.0
CA B:CYS16 4.7 66.2 1.0
N B:ALA18 4.7 63.9 1.0
CA B:HIS39 4.8 70.4 1.0
O B:ALA18 4.9 66.3 1.0

Zinc binding site 5 out of 6 in 5rlf

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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 Z235341991


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 Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:83.8
occ:1.00
 SG B:CYS5 2.3 75.0 1.0
SG B:CYS26 2.4 80.6 1.0
SG B:CYS29 2.6 75.6 1.0
CB B:CYS8 2.8 99.5 1.0
CB B:CYS29 3.0 74.1 1.0
SG B:CYS8 3.2 0.6 1.0
CB B:CYS26 3.4 77.5 1.0
CB B:CYS5 3.4 79.8 1.0
N B:CYS8 3.6 95.5 1.0
N B:CYS26 3.8 78.8 1.0
CA B:CYS8 3.9 97.3 1.0
CA B:CYS26 4.2 77.2 1.0
CA B:CYS29 4.2 72.4 1.0
N B:CYS29 4.2 73.6 1.0
CB B:LEU7 4.5 85.7 1.0
C B:LEU7 4.5 91.9 1.0
OG B:SER10 4.6 94.0 1.0
CB B:SER10 4.8 95.4 1.0
CA B:CYS5 4.8 80.6 1.0
C B:CYS8 4.8 98.0 1.0
N B:ASN9 4.8 1.0 1.0
CA B:LEU7 4.9 87.6 1.0
N B:LEU7 4.9 84.1 1.0
C B:CYS26 4.9 79.5 1.0
C B:LEU25 5.0 76.0 1.0
N B:GLY99 5.0 0.8 1.0

Zinc binding site 6 out of 6 in 5rlf

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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 Z235341991


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 Z235341991 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:0.4
occ:1.00
 SG B:CYS50 2.1 0.7 1.0
ND1 B:HIS75 2.3 0.0 1.0
SG B:CYS55 2.6 0.2 1.0
SG B:CYS72 3.0 0.1 1.0
CG B:HIS75 3.2 0.7 1.0
CB B:CYS50 3.2 0.8 1.0
CE1 B:HIS75 3.3 0.6 1.0
CB B:CYS55 3.4 0.3 1.0
CB B:HIS75 3.4 0.5 1.0
CB B:CYS72 3.4 97.3 1.0
N B:CYS72 3.7 94.4 1.0
CB B:ALA52 4.0 0.2 1.0
CA B:CYS72 4.1 98.4 1.0
CD2 B:HIS75 4.4 0.1 1.0
NE2 B:HIS75 4.4 0.6 1.0
N B:HIS75 4.4 0.4 1.0
CA B:HIS75 4.5 0.2 1.0
CA B:CYS50 4.6 0.0 1.0
CG2 B:VAL57 4.7 1.0 1.0
C B:TYR71 4.8 96.0 1.0
CA B:CYS55 4.8 0.5 1.0
CB B:VAL57 4.9 0.6 1.0
C B:CYS72 4.9 98.8 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 04:00:43 2024

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