Zinc in PDB 7b83: 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: 7b83 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)	23.93 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	113.357, 53.113, 44.891, 90, 102.98, 90
R / Rfree (%)	18.4 / 20.7

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 7b83). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total only one binding site of Zinc was determined in the Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc, PDB code: 7b83:

Zinc binding site 1 out of 1 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:56.6 occ:0.52 ZN2 A:PK8401 0.0 56.6 0.5 O01 A:PK8401 2.0 39.5 0.5 S03 A:PK8401 2.1 44.4 0.5 NE2 A:HIS41 2.1 31.1 1.0 SG A:CYS145 2.3 27.2 1.0 O A:HOH643 2.8 36.7 1.0 O A:HOH509 2.8 38.4 1.0 N09 A:PK8401 2.9 42.9 0.5 CE1 A:HIS41 2.9 29.1 1.0 C04 A:PK8401 2.9 41.9 0.5 HB2 A:CYS145 3.0 31.2 1.0 HE1 A:HIS41 3.0 35.0 1.0 CB A:CYS145 3.2 25.9 1.0 CD2 A:HIS41 3.2 31.2 1.0 HB3 A:CYS145 3.4 31.2 1.0 HD2 A:HIS41 3.5 37.5 1.0 O A:HIS164 3.8 30.6 1.0 HD22 A:LEU27 3.8 27.5 1.0 ND1 A:HIS41 4.1 29.2 1.0 C08 A:PK8401 4.2 40.1 0.5 CG A:HIS41 4.2 29.1 1.0 C05 A:PK8401 4.3 42.4 0.5 H A:CYS145 4.3 31.5 1.0 HD21 A:LEU27 4.5 27.5 1.0 O A:HOH529 4.5 43.2 1.0 H081 A:PK8401 4.5 48.2 0.5 CA A:CYS145 4.5 25.4 1.0 CD2 A:LEU27 4.6 22.8 1.0 O A:DMS403 4.6 55.5 1.0 H051 A:PK8401 4.7 51.0 0.5 HB3 A:LEU27 4.7 31.4 1.0 HD1 A:HIS41 4.8 35.1 1.0 H A:GLY143 4.8 35.1 1.0 N A:CYS145 4.9 26.1 1.0 HA A:CYS145 4.9 30.5 1.0 C A:HIS164 4.9 29.7 1.0 HA A:HIS164 4.9 25.4 1.0 H21 A:DMS403 4.9 60.3 1.0 S A:DMS403 5.0 68.7 1.0

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. Massive X-Ray Screening Reveals Two Allosteric Drug Binding Sites of Sars-Cov-2 Main Protease Biorxiv 2020.
DOI: 10.1101/2020.11.12.378422