Chlorine in PDB 7aga: Structure of Sars-Cov-2 Main Protease Bound to AT7519

All present enzymatic activity of Structure of Sars-Cov-2 Main Protease Bound to AT7519:
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 AT7519, PDB code: 7aga 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, H.Andaleeb, N.Werner, S.Falke, W.Hinrichs, B.Alvesfranca, M.Schwinzer, H.Brognaro, 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, J.Boger, 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)	30.93 / 1.68
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	112.372, 52.641, 44.585, 90.00, 102.67, 90.00
R / Rfree (%)	18.6 / 22.3

The binding sites of Chlorine atom in the Structure of Sars-Cov-2 Main Protease Bound to AT7519 (pdb code 7aga). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 4 binding sites of Chlorine where determined in the Structure of Sars-Cov-2 Main Protease Bound to AT7519, PDB code: 7aga:
Jump to Chlorine binding site number: 1; 2; 3; 4;

Chlorine binding site 1 out of 4 in the Structure of Sars-Cov-2 Main Protease Bound to AT7519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Structure of Sars-Cov-2 Main Protease Bound to AT7519 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:53.6 occ:0.72 CL1 A:LZE401 0.0 53.6 0.7 C23 A:LZE401 1.7 51.4 0.7 C17 A:LZE401 2.7 49.5 0.7 C22 A:LZE401 2.7 51.3 0.7 HD2 A:PRO293 2.7 24.9 1.0 H22 A:LZE401 2.8 61.5 0.7 HE2 A:PHE294 3.0 52.1 1.0 HG21 A:ILE249 3.0 38.0 1.0 C15 A:LZE401 3.0 44.7 0.7 H14 A:LZE401 3.1 54.1 0.7 HD13 A:ILE249 3.1 43.7 1.0 N14 A:LZE401 3.2 45.1 0.7 O A:HOH607 3.2 51.2 0.3 HD2 A:PHE294 3.4 50.0 1.0 HB A:THR292 3.4 26.2 1.0 HG2 A:PRO293 3.5 27.6 1.0 CD A:PRO293 3.6 20.7 1.0 CE2 A:PHE294 3.7 43.4 1.0 O16 A:LZE401 3.8 41.5 0.7 CD2 A:PHE294 3.9 41.7 1.0 CG2 A:ILE249 3.9 31.7 1.0 C18 A:LZE401 4.0 51.4 0.7 C21 A:LZE401 4.0 51.5 0.7 CG A:PRO293 4.0 23.0 1.0 CD1 A:ILE249 4.1 36.4 1.0 HD3 A:PRO293 4.1 24.9 1.0 C13 A:LZE401 4.1 46.5 0.7 HG22 A:ILE249 4.2 38.0 1.0 HB2 A:PRO293 4.2 29.3 1.0 O8 A:LZE401 4.2 48.5 0.7 HD12 A:ILE249 4.3 43.7 1.0 CB A:THR292 4.3 21.9 1.0 HG23 A:ILE249 4.4 38.0 1.0 HG21 A:VAL202 4.4 26.1 1.0 C20 A:LZE401 4.5 51.8 0.7 HG11 A:VAL202 4.5 29.1 1.0 H A:PHE294 4.5 29.1 1.0 HG22 A:VAL202 4.5 26.1 1.0 N A:PRO293 4.6 21.2 1.0 HD11 A:ILE249 4.6 43.7 1.0 HG22 A:THR292 4.6 50.6 1.0 HG21 A:THR292 4.7 50.6 1.0 CB A:PRO293 4.7 24.4 1.0 H21 A:LZE401 4.7 61.8 0.7 HG13 A:VAL202 4.7 29.1 1.0 CG2 A:THR292 4.8 42.1 1.0 HA A:THR292 4.8 26.5 1.0 CB A:ILE249 4.8 29.6 1.0 HG1 A:THR292 4.8 27.5 1.0 HB A:ILE249 4.8 35.6 1.0 HG3 A:PRO293 4.9 27.6 1.0 C7 A:LZE401 4.9 47.0 0.7 CG1 A:ILE249 4.9 33.8 1.0 CZ A:PHE294 4.9 44.4 1.0 C9 A:LZE401 4.9 47.2 0.7 HG12 A:ILE249 4.9 40.5 1.0 CG2 A:VAL202 5.0 21.7 1.0 HD2 A:HIS246 5.0 34.5 1.0

Chlorine binding site 2 out of 4 in the Structure of Sars-Cov-2 Main Protease Bound to AT7519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Structure of Sars-Cov-2 Main Protease Bound to AT7519 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl401 b:51.4 occ:0.72 CL7 A:LZE401 0.0 51.4 0.7 C18 A:LZE401 1.7 51.4 0.7 C17 A:LZE401 2.7 49.5 0.7 C20 A:LZE401 2.7 51.8 0.7 H20 A:LZE401 2.8 62.1 0.7 O A:HOH687 2.9 55.5 1.0 C15 A:LZE401 2.9 44.7 0.7 HB2 A:GLN107 3.0 50.4 1.0 O16 A:LZE401 3.2 41.5 0.7 HG3 A:GLN110 3.4 47.3 1.0 O A:HOH611 3.5 40.8 1.0 N14 A:LZE401 3.7 45.1 0.7 O A:PRO108 3.7 27.9 1.0 HG2 A:GLN110 3.7 47.3 1.0 CB A:GLN107 3.8 42.0 1.0 HB3 A:GLN107 3.8 50.4 1.0 HG3 A:GLN107 3.9 59.5 1.0 C23 A:LZE401 4.0 51.4 0.7 CG A:GLN110 4.0 39.4 1.0 H14 A:LZE401 4.0 54.1 0.7 C21 A:LZE401 4.0 51.5 0.7 O A:HOH597 4.0 41.8 1.0 O A:HOH682 4.2 38.3 1.0 CG A:GLN107 4.4 49.6 1.0 CD A:GLN110 4.5 44.0 1.0 C22 A:LZE401 4.5 51.3 0.7 HE2 A:HIS246 4.6 35.8 1.0 C13 A:LZE401 4.6 46.5 0.7 O A:HOH607 4.7 51.2 0.3 H21 A:LZE401 4.7 61.8 0.7 HE21 A:GLN107 4.7 73.2 1.0 OE1 A:GLN110 4.7 43.3 1.0 H A:GLN110 4.8 31.4 1.0 H12 A:LZE401 4.8 56.0 0.7 C A:PRO108 4.9 27.2 1.0 HA3 A:GLY109 4.9 29.8 1.0 O A:HOH695 4.9 43.0 1.0 CA A:GLN107 4.9 35.1 1.0 C A:GLN107 4.9 31.1 1.0

Chlorine binding site 3 out of 4 in the Structure of Sars-Cov-2 Main Protease Bound to AT7519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of Structure of Sars-Cov-2 Main Protease Bound to AT7519 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl402 b:32.0 occ:0.50 H A:ALA285 2.4 40.3 1.0 HG A:LEU286 2.9 49.2 1.0 H A:LEU286 3.2 35.7 1.0 N A:ALA285 3.2 33.6 1.0 HA A:SER284 3.3 37.5 1.0 HB3 A:ALA285 3.4 41.7 1.0 HB3 A:SER284 3.6 41.8 1.0 N A:LEU286 3.8 29.7 1.0 CG A:LEU286 3.8 41.0 1.0 CA A:SER284 3.9 31.2 1.0 CA A:ALA285 4.0 33.4 1.0 C A:SER284 4.0 31.5 1.0 HD23 A:LEU286 4.1 50.3 1.0 CB A:ALA285 4.1 34.8 1.0 CB A:SER284 4.2 34.8 1.0 C A:ALA285 4.2 33.0 1.0 HD21 A:LEU286 4.4 50.3 1.0 CD2 A:LEU286 4.4 41.9 1.0 HD12 A:LEU286 4.5 50.2 1.0 HB2 A:ALA285 4.5 41.7 1.0 HB3 A:LEU286 4.6 46.0 1.0 CB A:LEU286 4.6 38.4 1.0 CD1 A:LEU286 4.7 41.8 1.0 OG A:SER284 4.7 40.5 1.0 CA A:LEU286 4.8 33.1 1.0 OE2 A:GLU288 4.8 47.2 1.0 O A:HOH677 4.8 41.9 1.0 HD11 A:LEU286 4.8 50.2 1.0 HB1 A:ALA285 4.9 41.7 1.0 HA A:ALA285 4.9 40.0 1.0

Chlorine binding site 4 out of 4 in the Structure of Sars-Cov-2 Main Protease Bound to AT7519


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of Structure of Sars-Cov-2 Main Protease Bound to AT7519 within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl403 b:75.7 occ:1.00 H A:TYR54 2.3 33.6 1.0 HA A:ASN53 2.8 41.7 1.0 HD2 A:TYR54 2.9 30.1 1.0 HH22 A:ARG188 3.0 55.5 0.6 N A:TYR54 3.1 28.0 1.0 HB2 A:TYR54 3.3 31.5 1.0 OE1 A:GLU55 3.4 29.4 0.5 O A:PRO52 3.6 31.8 1.0 CA A:ASN53 3.6 34.8 1.0 CD2 A:TYR54 3.8 25.1 1.0 NH2 A:ARG188 3.8 46.2 0.6 C A:ASN53 3.9 29.4 1.0 H A:GLU55 3.9 38.2 0.5 H A:GLU55 4.0 38.2 0.5 HH21 A:ARG188 4.0 55.5 0.6 CB A:TYR54 4.0 26.2 1.0 HH22 A:ARG40 4.1 36.4 1.0 HH12 A:ARG40 4.2 26.9 1.0 CA A:TYR54 4.2 27.8 1.0 OD1 A:ASN53 4.3 43.2 1.0 CD A:GLU55 4.3 34.9 0.5 C A:PRO52 4.4 32.3 1.0 CG A:TYR54 4.4 25.1 1.0 O A:HOH502 4.4 33.2 1.0 N A:ASN53 4.5 33.6 1.0 CG A:ASN53 4.5 42.0 1.0 OE2 A:GLU55 4.5 37.2 0.5 NH2 A:ARG40 4.6 30.3 1.0 NH1 A:ARG40 4.6 22.4 1.0 HH11 A:ARG188 4.6 56.2 0.6 CB A:ASN53 4.6 39.0 1.0 N A:GLU55 4.7 31.8 0.5 N A:GLU55 4.7 31.9 0.5 CE2 A:TYR54 4.8 29.2 1.0 HE2 A:TYR54 4.8 35.0 1.0 HH21 A:ARG188 4.8 57.1 0.4 HB3 A:TYR54 4.9 31.5 1.0 HA A:TYR54 4.9 33.3 1.0 CZ A:ARG40 4.9 27.1 1.0 CZ A:ARG188 4.9 47.5 0.6 HB2 A:ASN53 5.0 46.8 1.0 C A:TYR54 5.0 28.7 1.0

S.Guenther, P.Y.A., Reinke, Y., Fernandez-Garcia, J., Lieske, T.J., Lane, H.M., Ginn, F.H.M., Koua, C., Ehrt, W., Ewert, D., Oberthuer, O., Yefanov, S., Meier, K., Lorenzen, B., Krichel, J.D., Kopicki, L., Gelisio, W., Brehm, I., Dunkel, B., Seychell, H., Gieseler, B., Norton-Baker, B., Escudero-Perez, M., Domaracky, S., Saouane, A., Tolstikova, T.A., White, A., Hanle, M., Groessler, H., Fleckenstein, F., Trost, M., Galchenkova, Y., Gevorkov, C., Li, S., Awel, A.Peck, M., Barthelmess, F., Schluenzen, L.X., Paulraj, N., Werner, H., Andaleeb, N., Ullah, S., Falke, V., Srinivasan, B., Franca, M., Schwinzer, H., Brognaro, C., Rogers, D., Melo, J.J., Doyle, J., Knoska, G.E., Pena Murillo, A., Rahmani Mashhour, F., Guicking, V., Hennicke, P., Fischer, J., Hakanpaeae, J., Meyer, P., Gribbon, B., Ellinger, M., Kuzikov, M., Wolf, G., Burenkov, D., Von Stetten, G., Pompidor, I., Bento, S., Panneerselvam, I., Karpics, T.R., Schneider, M., Garcia Alai, S., Niebling, C., Guenther, C., Schmidt, R., Schubert, H., Han, J., Boger, D., Monteiro, L., Zhang, X., Sun, J., Pletzer-Zelgert, J., Wollenhaupt, C., Feiler, M., Weiss, E.C., Schulz, P., Mehrabi, K., Karnicar, A., Usenik, J., Loboda, H., Tidow, A., Chari, R., Hilgenfeld, C., Uetrecht, R., Cox, A., Zaliani, T., Beck, M., Rarey, S., Guenther, D., Turk, W., Hinrichs, H.N., Chapman, A., Pearson, C., Betzel, A.Meents. Inhibition of Sars-Cov-2 Main Protease By Allosteric Drug-Binding Biorxiv 2020.
DOI: 10.1101/2020.11.12.378422