Zinc in PDB 6yt8: Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc:
2.7.7.48; 3.4.19.12; 3.4.22.69; 3.6.4.12; 3.6.4.13;

The structure of Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc, PDB code: 6yt8 was solved by S.Guenther, P.Reinke, D.Oberthuer, O.Yefanov, L.Gelisio, H.Ginn, J.Lieske, M.Domaracky, W.Brehm, A.Rahmani Mashour, T.A.White, J.Knoska, G.Penaesperanza, F.Koua, A.Tolstikova, M.Groessler, P.Fischer, V.Hennicke, H.Fleckenstein, F.Trost, M.Galchenkova, Y.Gevorkov, C.Li, S.Awel, L.X.Paulraj, N.Ullah, S.Falke, B.Alves Franca, M.Schwinzer, H.Brognaro, N.Werner, M.Perbandt, H.Tidow, B.Seychell, T.Beck, S.Meier, J.J.Doyle, H.Giseler, D.Melo, I.Dunkel, T.J.Lane, A.Peck, S.Saouane, J.Hakanpaeae, J.Meyer, H.Noei, P.Gribbon, B.Ellinger, M.Kuzikov, M.Wolf, L.Zhang, C.Ehrt, J.Pletzer-Zelgert, J.Wollenhaupt, C.Feiler, M.Weiss, E.C.Schulz, P.Mehrabi, B.Norton-Baker, C.Schmidt, K.Lorenzen, R.Schubert, H.Han, A.Chari, Y.Fernandez Garcia, D.Turk, R.Hilgenfeld, M.Rarey, A.Zaliani, H.N.Chapman, A.Pearson, C.Betzel, A.Meents, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.06 / 2.05
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.659, 53.438, 44.446, 90.00, 103.03, 90.00
R / Rfree (%)	20.2 / 23.7

The structure of Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc (pdb code 6yt8). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc, PDB code: 6yt8:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:47.6 occ:0.73 ZN2 A:PK8401 0.0 47.6 0.7 O01 A:PK8401 0.8 48.4 0.3 N09 A:PK8401 1.1 49.8 0.3 C04 A:PK8401 2.0 53.6 0.3 O01 A:PK8401 2.0 47.5 0.7 S03 A:PK8401 2.1 57.0 0.7 C08 A:PK8401 2.1 47.5 0.3 NE2 A:HIS41 2.1 38.7 1.0 SG A:CYS145 2.2 34.0 1.0 ZN2 A:PK8401 2.3 52.1 0.3 H081 A:PK8401 2.4 57.0 0.3 S03 A:PK8401 2.8 55.0 0.3 N09 A:PK8401 2.9 48.8 0.7 C04 A:PK8401 3.0 52.1 0.7 CE1 A:HIS41 3.0 36.7 1.0 HE1 A:HIS41 3.1 44.1 1.0 CD2 A:HIS41 3.2 39.0 1.0 HB2 A:CYS145 3.2 39.2 1.0 C05 A:PK8401 3.3 52.1 0.3 C07 A:PK8401 3.3 47.5 0.3 CB A:CYS145 3.3 32.7 1.0 HD2 A:HIS41 3.4 46.7 1.0 HB3 A:CYS145 3.5 39.2 1.0 O A:HIS164 3.6 38.5 1.0 C06 A:PK8401 3.7 50.9 0.3 H051 A:PK8401 4.0 62.6 0.3 H071 A:PK8401 4.0 57.0 0.3 ND1 A:HIS41 4.1 37.6 1.0 C08 A:PK8401 4.2 49.2 0.7 CG A:HIS41 4.2 35.3 1.0 HD22 A:LEU27 4.2 33.5 1.0 HD21 A:LEU27 4.3 33.5 1.0 C05 A:PK8401 4.3 52.1 0.7 H A:CYS145 4.4 35.5 1.0 H081 A:PK8401 4.5 59.0 0.7 H061 A:PK8401 4.6 61.1 0.3 CA A:CYS145 4.7 30.9 1.0 H051 A:PK8401 4.7 62.5 0.7 C A:HIS164 4.7 35.7 1.0 CD2 A:LEU27 4.8 27.9 1.0 O A:DMS403 4.8 53.5 1.0 HA A:HIS164 4.8 40.0 1.0 HD1 A:HIS41 4.8 45.1 1.0 H21 A:DMS403 4.8 63.2 1.0 HB3 A:LEU27 4.8 36.0 1.0 H A:GLY143 4.9 43.8 1.0 N A:CYS145 5.0 29.6 1.0 S A:DMS403 5.0 68.1 1.0

Zinc binding site 2 out of 2 in the Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn401 b:52.1 occ:0.28 ZN2 A:PK8401 0.0 52.1 0.3 O01 A:PK8401 2.0 48.4 0.3 S03 A:PK8401 2.1 55.0 0.3 ZN2 A:PK8401 2.3 47.6 0.7 S03 A:PK8401 2.5 57.0 0.7 O A:HIS164 2.6 38.5 1.0 SG A:CYS145 2.8 34.0 1.0 N09 A:PK8401 2.9 49.8 0.3 C04 A:PK8401 2.9 53.6 0.3 HA A:MET165 3.0 45.0 0.7 HA A:MET165 3.1 45.0 0.3 O A:DMS403 3.2 53.5 1.0 H21 A:DMS403 3.2 63.2 1.0 O A:HOH610 3.2 39.3 1.0 HE1 A:HIS41 3.7 44.1 1.0 C A:HIS164 3.7 35.7 1.0 NE2 A:HIS41 3.7 38.7 1.0 S A:DMS403 3.7 68.1 1.0 CE1 A:HIS41 3.9 36.7 1.0 CA A:MET165 3.9 37.5 0.7 C2 A:DMS403 4.0 52.6 1.0 CA A:MET165 4.0 37.5 0.3 SD A:MET165 4.0 33.7 0.3 C04 A:PK8401 4.1 52.1 0.7 C08 A:PK8401 4.2 47.5 0.3 O01 A:PK8401 4.2 47.5 0.7 N A:MET165 4.2 36.8 0.7 N A:MET165 4.2 36.7 0.3 C05 A:PK8401 4.3 52.1 0.3 HB3 A:MET165 4.3 44.4 0.7 CB A:CYS145 4.5 32.7 1.0 H081 A:PK8401 4.5 57.0 0.3 H A:GLU166 4.6 45.2 1.0 H23 A:DMS403 4.6 63.2 1.0 N09 A:PK8401 4.6 48.8 0.7 CB A:MET165 4.7 37.0 0.7 CD2 A:HIS41 4.7 39.0 1.0 H22 A:DMS403 4.7 63.2 1.0 HA A:HIS164 4.7 40.0 1.0 HB3 A:CYS145 4.7 39.2 1.0 H051 A:PK8401 4.7 62.6 0.3 HB2 A:CYS145 4.8 39.2 1.0 ND1 A:HIS41 4.8 37.6 1.0 C A:MET165 4.8 38.2 0.3 C A:MET165 4.9 38.2 0.7 CA A:HIS164 4.9 33.3 1.0 CB A:MET165 4.9 37.0 0.3 CG A:MET165 4.9 36.4 0.3 HB3 A:MET165 4.9 44.4 0.3 HG2 A:MET165 5.0 43.7 0.3 O A:HOH643 5.0 42.9 1.0 N A:GLU166 5.0 37.7 1.0 HB2 A:MET165 5.0 44.4 0.7

S.Guenther, P.Reinke, D.Oberthuer, O.Yefanov, L.Gelisio, H.Ginn, J.Lieske, W.Brehm, A.Rahmani Mashour, J.Knoska, G.Pena Esperanza, F.Koua, A.Tolstikova, M.Groessler, H.Fleckenstein, F.Trost, M.Galchenkova, Y.Gevorkov, C.Li, S.Awel, L.X.Paulraj, N.Ullah, S.Falke, B.Alves Franca, M.Schwinzer, H.Brognaro, N.Werner, M.Perbandt, B.Seychell, S.Meier, H.Giseler, D.Melo, I.Dunkel, T.J.Lane, A.Peck, S.Saouane, J.Hakanpaeae, J.Meyer, H.Noei, P.Gribbon, B.Ellinger, M.Kuzikov, M.Wolf, L.Zhang, C.Ehrt, J.Pletzer-Zelgert, J.Wollenhaupt, C.Feiler, M.Weiss, E.C.Schulz, P.Mehrabi, B.Norton-Baker, C.Schmidt, K.Lorenzen, R.Schubert, H.Han, A.Chari, Y.Fernandez Garcia, R.Hilgenfeld, M.Rarey, A.Zaliani, H.N.Chapman, A.Pearson, C.Betzel, A.Meents. Structure of Sars-Cov-2 Main Protease Bound 2-Methyl-1-Tetralone. To Be Published.