Atomistry » Zinc » PDB 7tzj-7ubn » 7tzj
Atomistry »
  Zinc »
    PDB 7tzj-7ubn »
      7tzj »

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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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

Go back to Zinc Binding Sites List in 7tzj
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: Sat Apr 8 03:53:12 2023

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy