Zinc in PDB 7tzj: Sars Cov-2 Plpro in Complex with Inhibitor 3K

Enzymatic activity of Sars Cov-2 Plpro in Complex with Inhibitor 3K

All present enzymatic activity of Sars Cov-2 Plpro in Complex with Inhibitor 3K:
3.4.19.12;

Protein crystallography data

The structure of Sars Cov-2 Plpro in Complex with Inhibitor 3K, PDB code: 7tzj was solved by D.J.Calleja, T.Klemm, B.C.Lechtenberg, N.W.Kuchel, G.Lessene, D.Komander, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.49 / 2.66
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 72.951, 90.632, 99.766, 90, 90, 90
R / Rfree (%) 20.1 / 25.7

Other elements in 7tzj:

The structure of Sars Cov-2 Plpro in Complex with Inhibitor 3K also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Zinc Binding Sites:

The binding sites of Zinc atom in the Sars Cov-2 Plpro in Complex with Inhibitor 3K (pdb code 7tzj). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 9 binding sites of Zinc where determined in the Sars Cov-2 Plpro in Complex with Inhibitor 3K, PDB code: 7tzj:
Jump to Zinc binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Zinc binding site 1 out of 9 in 7tzj

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Zinc binding site 1 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn402

b:104.7
occ:1.00
 NE2 A:HIS47 2.3 94.0 1.0
CD2 A:HIS47 3.2 89.9 1.0
CE1 A:HIS47 3.4 89.3 1.0
CG A:HIS47 4.4 74.1 1.0
ND1 A:HIS47 4.4 84.2 1.0

Zinc binding site 2 out of 9 in 7tzj

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Zinc binding site 2 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn403

b:88.3
occ:1.00
 ND1 A:HIS89 2.3 52.8 1.0
CE1 A:HIS89 3.2 59.1 1.0
CG A:HIS89 3.4 53.3 1.0
OD2 A:ASP108 3.7 48.4 1.0
CB A:HIS89 3.8 48.4 1.0
OD1 A:ASP108 4.2 62.9 1.0
CG A:ASP108 4.3 56.3 1.0
NE2 A:HIS89 4.3 55.7 1.0
CA A:HIS89 4.4 46.8 1.0
CD2 A:HIS89 4.5 60.3 1.0
O A:HOH516 4.8 60.8 1.0

Zinc binding site 3 out of 9 in 7tzj

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Zinc binding site 3 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn404

b:66.8
occ:1.00
 NE2 A:HIS73 2.2 65.0 1.0
O A:HOH517 2.4 58.8 1.0
O A:HOH515 2.8 38.7 1.0
CE1 A:HIS73 2.9 60.4 1.0
CD2 A:HIS73 3.3 60.1 1.0
O A:HOH514 3.9 47.9 1.0
ND1 A:HIS73 4.1 50.3 1.0
CG A:HIS73 4.3 54.5 1.0
O A:GLU70 4.4 59.0 1.0
CD A:PRO130 4.7 53.0 1.0
CA A:GLU70 5.0 50.4 1.0

Zinc binding site 4 out of 9 in 7tzj

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Zinc binding site 4 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn405

b:46.0
occ:1.00
 OE2 A:GLU67 2.0 52.0 1.0
NE2 A:HIS17 2.1 48.4 1.0
O A:HOH511 2.6 37.9 1.0
CD A:GLU67 2.9 49.2 1.0
CE1 A:HIS17 3.0 49.7 1.0
CD2 A:HIS17 3.1 49.9 1.0
OE1 A:GLU67 3.2 53.7 1.0
CG2 A:THR63 4.1 40.0 1.0
ND1 A:HIS17 4.1 50.8 1.0
CB A:ASN15 4.2 39.5 1.0
CG A:HIS17 4.2 48.4 1.0
CG A:GLU67 4.3 49.0 1.0
CD2 A:LEU64 4.6 56.5 1.0
CG A:ASN15 4.8 52.1 1.0
OD1 A:ASN15 5.0 39.8 1.0

Zinc binding site 5 out of 9 in 7tzj

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Zinc binding site 5 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 5 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn402

b:105.7
occ:1.00
 ND1 B:HIS89 2.2 72.9 1.0
CE1 B:HIS89 3.1 69.8 1.0
OD2 B:ASP108 3.2 61.7 1.0
CG B:HIS89 3.2 60.8 1.0
CB B:HIS89 3.6 59.1 1.0
CG B:ASP108 4.0 59.9 1.0
OD1 B:ASP108 4.0 68.6 1.0
CA B:HIS89 4.1 54.6 1.0
NE2 B:HIS89 4.3 53.3 1.0
CD2 B:HIS89 4.4 60.3 1.0
O B:HIS89 4.6 51.5 1.0
CG1 B:VAL159 4.7 63.4 1.0
C B:HIS89 4.8 50.9 1.0
NE1 B:TRP93 5.0 58.7 1.0

Zinc binding site 6 out of 9 in 7tzj

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Zinc binding site 6 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 6 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn403

b:86.7
occ:1.00
 NE2 B:HIS255 2.3 74.5 1.0
CE1 B:HIS255 2.9 87.7 1.0
CD2 B:HIS255 3.5 74.0 1.0
ND1 B:HIS255 4.1 75.2 1.0
CG B:HIS255 4.5 78.7 1.0

Zinc binding site 7 out of 9 in 7tzj

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Zinc binding site 7 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 7 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn404

b:45.7
occ:1.00
 OE2 B:GLU67 1.9 49.8 1.0
NE2 B:HIS17 2.0 50.5 1.0
CD2 B:HIS17 3.0 54.2 1.0
CE1 B:HIS17 3.0 43.2 1.0
CD B:GLU67 3.0 45.2 1.0
OE1 B:GLU67 3.5 46.8 1.0
ND1 B:HIS17 4.1 45.1 1.0
CG B:HIS17 4.1 51.3 1.0
CG2 B:THR63 4.2 41.6 1.0
CG B:GLU67 4.3 42.2 1.0
CB B:ASN15 4.4 48.3 1.0
CD2 B:LEU64 4.6 51.5 1.0

Zinc binding site 8 out of 9 in 7tzj

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Zinc binding site 8 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 8 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn405

b:60.8
occ:1.00
 NE2 B:HIS47 2.2 48.5 1.0
O B:HOH511 2.2 39.3 1.0
O B:HOH509 2.4 35.9 1.0
CE1 B:HIS47 3.1 48.9 1.0
CD2 B:HIS47 3.2 47.6 1.0
ND1 B:HIS47 4.2 44.8 1.0
CG B:HIS47 4.3 52.9 1.0

Zinc binding site 9 out of 9 in 7tzj

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Zinc binding site 9 out of 9 in the Sars Cov-2 Plpro in Complex with Inhibitor 3K


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 9 of Sars Cov-2 Plpro in Complex with Inhibitor 3K within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn406

b:77.8
occ:1.00
 NE2 B:HIS73 2.3 64.8 1.0
CE1 B:HIS73 3.0 58.9 1.0
CD2 B:HIS73 3.4 53.2 1.0
O B:GLU70 4.1 47.0 1.0
ND1 B:HIS73 4.3 51.6 1.0
CG B:HIS73 4.5 57.3 1.0
CD B:PRO130 4.6 62.2 1.0
CG B:PRO130 4.9 47.1 1.0
C B:GLU70 5.0 49.0 1.0
CA B:GLU70 5.0 50.8 1.0

Reference:

D.J.Calleja, N.Kuchel, B.G.C.Lu, R.W.Birkinshaw, T.Klemm, M.Doerflinger, J.P.Cooney, L.Mackiewicz, A.E.Au, Y.Q.Yap, T.R.Blackmore, K.Katneni, E.Crighton, J.Newman, K.E.Jarman, M.J.Call, B.C.Lechtenberg, P.E.Czabotar, M.Pellegrini, S.A.Charman, K.N.Lowes, J.P.Mitchell, U.Nachbur, G.Lessene, D.Komander. Insights Into Drug Repurposing, As Well As Specificity and Compound Properties of Piperidine-Based Sars-Cov-2 Plpro Inhibitors. Front Chem V. 10 61209 2022.
ISSN: ESSN 2296-2646
PubMed: 35494659
DOI: 10.3389/FCHEM.2022.861209
Page generated: Wed Oct 30 11:47:56 2024

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