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Zinc in PDB 5rm1: Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z426041412

Enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z426041412

All present enzymatic activity of Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z426041412:
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 Z426041412, PDB code: 5rm1 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) 81.33 / 1.90
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 59.317, 70.174, 85.160, 102.40, 96.07, 112.75
R / Rfree (%) 17.6 / 23.4

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 Z426041412 (pdb code 5rm1). 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 Z426041412, PDB code: 5rm1:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6;

Zinc binding site 1 out of 6 in 5rm1

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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 Z426041412


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 Z426041412 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn701

b:55.2
occ:1.00
 SG A:CYS50 2.2 53.4 1.0
SG A:CYS55 2.3 54.2 1.0
ND1 A:HIS75 2.3 53.5 1.0
SG A:CYS72 2.7 56.8 1.0
CB A:CYS50 3.2 55.7 1.0
CB A:CYS55 3.3 57.6 1.0
CG A:HIS75 3.3 52.7 1.0
CE1 A:HIS75 3.3 54.8 1.0
CB A:CYS72 3.5 54.2 1.0
CB A:HIS75 3.5 50.3 1.0
N A:CYS72 3.8 54.5 1.0
CA A:CYS72 4.2 54.5 1.0
CB A:ALA52 4.2 54.0 1.0
N A:HIS75 4.4 54.0 1.0
CD2 A:HIS75 4.5 54.1 1.0
NE2 A:HIS75 4.5 55.8 1.0
CA A:CYS50 4.6 55.5 1.0
CA A:HIS75 4.6 52.1 1.0
CA A:CYS55 4.7 60.0 1.0
CG2 A:VAL57 4.7 54.0 1.0
CB A:VAL57 4.7 54.9 1.0
C A:TYR71 4.9 51.2 1.0

Zinc binding site 2 out of 6 in 5rm1

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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 Z426041412


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 Z426041412 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn702

b:50.5
occ:1.00
 ND1 A:HIS39 1.9 52.7 1.0
NE2 A:HIS33 2.0 43.1 1.0
SG A:CYS19 2.2 50.0 1.0
SG A:CYS16 2.3 53.0 1.0
CE1 A:HIS39 2.9 53.9 1.0
CE1 A:HIS33 2.9 43.2 1.0
CG A:HIS39 3.0 53.6 1.0
CD2 A:HIS33 3.2 44.7 1.0
N A:CYS19 3.2 48.4 1.0
CB A:CYS16 3.3 52.1 1.0
CB A:HIS39 3.4 53.0 1.0
CB A:CYS19 3.4 45.6 1.0
CA A:CYS19 3.7 48.8 1.0
C A:ALA18 4.0 49.7 1.0
NE2 A:HIS39 4.1 54.8 1.0
ND1 A:HIS33 4.1 44.7 1.0
CD2 A:HIS39 4.1 54.9 1.0
CG A:HIS33 4.2 45.9 1.0
CB A:ALA18 4.3 46.2 1.0
CB A:ALA110 4.4 43.4 1.0
CA A:ALA18 4.5 48.6 1.0
CA A:CYS16 4.7 52.8 1.0
N A:ALA18 4.7 49.4 1.0
O A:ALA18 4.8 51.0 1.0
CA A:HIS39 4.9 52.8 1.0
CE2 A:PHE106 4.9 48.9 1.0
CZ A:PHE106 4.9 49.9 1.0

Zinc binding site 3 out of 6 in 5rm1

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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 Z426041412


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 Z426041412 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn703

b:59.0
occ:1.00
 SG A:CYS26 2.3 62.7 1.0
SG A:CYS29 2.4 62.1 1.0
SG A:CYS8 2.5 72.9 1.0
SG A:CYS5 2.5 57.3 1.0
CB A:CYS29 3.1 60.6 1.0
CB A:CYS26 3.1 59.8 1.0
CB A:CYS5 3.3 61.9 1.0
CB A:CYS8 3.5 68.8 1.0
N A:CYS26 3.7 57.1 1.0
N A:CYS8 3.7 68.7 1.0
CA A:CYS26 3.9 60.2 1.0
CA A:CYS8 4.1 69.9 1.0
N A:CYS29 4.2 59.6 1.0
CA A:CYS29 4.3 57.9 1.0
CB A:LEU7 4.5 64.9 1.0
C A:CYS26 4.6 62.1 1.0
C A:CYS8 4.7 71.6 1.0
CB A:SER10 4.7 71.3 1.0
C A:LEU7 4.7 66.5 1.0
O A:CYS26 4.7 62.4 1.0
CA A:CYS5 4.8 60.9 1.0
C A:LEU25 4.9 55.9 1.0
N A:SER10 4.9 74.4 1.0
N A:LEU7 4.9 63.6 1.0
CA A:LEU7 4.9 64.4 1.0
N A:ASN9 4.9 72.9 1.0
OG A:SER10 4.9 65.0 1.0

Zinc binding site 4 out of 6 in 5rm1

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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 Z426041412


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 Z426041412 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn702

b:52.3
occ:1.00
 NE2 B:HIS33 1.9 45.5 1.0
ND1 B:HIS39 2.0 45.3 1.0
SG B:CYS16 2.1 46.8 1.0
SG B:CYS19 2.5 53.7 1.0
CE1 B:HIS33 2.9 45.5 1.0
CD2 B:HIS33 3.0 46.8 1.0
CE1 B:HIS39 3.0 45.7 1.0
CG B:HIS39 3.0 46.2 1.0
CB B:CYS16 3.1 46.5 1.0
CB B:HIS39 3.4 46.6 1.0
CB B:CYS19 3.4 53.1 1.0
N B:CYS19 3.4 54.8 1.0
CA B:CYS19 3.8 52.8 1.0
ND1 B:HIS33 4.0 44.6 1.0
CG B:HIS33 4.1 46.7 1.0
NE2 B:HIS39 4.2 45.3 1.0
CD2 B:HIS39 4.2 45.4 1.0
C B:ALA18 4.2 55.1 1.0
CB B:ALA18 4.4 52.5 1.0
CB B:ALA110 4.5 40.3 1.0
CA B:CYS16 4.5 48.2 1.0
CA B:ALA18 4.6 53.9 1.0
N B:ALA18 4.6 54.0 1.0
CA B:HIS39 4.8 47.2 1.0
C B:CYS16 4.8 49.4 1.0
CE2 B:PHE106 4.9 44.2 1.0
O B:CYS16 5.0 47.2 1.0
CZ B:PHE106 5.0 44.0 1.0

Zinc binding site 5 out of 6 in 5rm1

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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 Z426041412


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 Z426041412 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn703

b:66.7
occ:1.00
 SG B:CYS5 2.4 62.2 1.0
SG B:CYS29 2.5 61.3 1.0
SG B:CYS8 2.5 62.0 1.0
SG B:CYS26 2.6 52.6 1.0
CB B:CYS29 2.9 60.5 1.0
CB B:CYS8 3.5 67.1 1.0
CB B:CYS26 3.5 53.5 1.0
CB B:CYS5 3.5 65.3 1.0
N B:CYS8 3.8 68.9 1.0
N B:CYS26 3.9 55.2 1.0
CA B:GLY99 3.9 65.0 1.0
N B:GLY99 4.0 66.9 1.0
N B:CYS29 4.0 58.5 1.0
CA B:CYS29 4.1 57.5 1.0
CA B:CYS8 4.2 67.0 1.0
CA B:CYS26 4.2 52.2 1.0
C B:GLY99 4.4 65.0 1.0
OG B:SER100 4.6 56.4 1.0
CB B:LEU7 4.8 73.1 1.0
C B:CYS8 4.8 68.5 1.0
N B:ASN9 4.9 68.8 1.0
C B:CYS26 4.9 53.0 1.0
N B:SER100 4.9 62.9 1.0
CA B:CYS5 4.9 62.9 1.0
C B:LEU7 4.9 69.6 1.0
O B:CYS26 4.9 47.4 1.0
O B:GLY99 4.9 63.1 1.0
CB B:SER10 5.0 67.5 1.0

Zinc binding site 6 out of 6 in 5rm1

Go back to Zinc Binding Sites List in 5rm1
Zinc binding site 6 out of 6 in the Pandda Analysis Group Deposition -- Crystal Structure of Sars-Cov-2 Helicase in Complex with Z426041412


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 Z426041412 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn704

b:82.1
occ:1.00
 SG B:CYS50 2.2 71.4 1.0
SG B:CYS55 2.4 98.0 1.0
ND1 B:HIS75 2.4 84.6 1.0
SG B:CYS72 2.7 71.6 1.0
CB B:CYS50 3.2 69.2 1.0
CB B:CYS55 3.2 0.1 1.0
CB B:CYS72 3.3 71.3 1.0
CG B:HIS75 3.4 83.1 1.0
CE1 B:HIS75 3.5 85.5 1.0
CB B:HIS75 3.5 79.8 1.0
N B:CYS72 3.7 70.0 1.0
CA B:CYS72 4.1 70.8 1.0
CB B:ALA52 4.2 86.8 1.0
N B:HIS75 4.4 77.4 1.0
CD2 B:HIS75 4.6 84.9 1.0
CA B:HIS75 4.6 78.5 1.0
CA B:CYS50 4.6 69.6 1.0
NE2 B:HIS75 4.6 86.0 1.0
CG2 B:VAL57 4.6 68.0 1.0
CB B:VAL57 4.6 71.8 1.0
CA B:CYS55 4.7 0.0 1.0
C B:TYR71 4.8 70.3 1.0
C B:CYS72 4.9 71.9 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: Thu Aug 21 07:21:04 2025

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