Chlorine in PDB 7b83: Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc

Enzymatic activity of 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;

Protein crystallography data

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

Other elements in 7b83:

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

Zinc (Zn) 1 atom

Chlorine Binding Sites:

The binding sites of Chlorine 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 Chlorine atom.
In total only one binding site of Chlorine was determined in the Structure of Sars-Cov-2 Main Protease Bound to Pyrithione Zinc, PDB code: 7b83:

Chlorine binding site 1 out of 1 in 7b83

Go back to Chlorine Binding Sites List in 7b83
Chlorine 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 Chlorine with other atoms in the Cl 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:Cl404

b:46.3
occ:1.00
HE21 A:GLN127 2.6 36.6 1.0
HG2 A:GLN127 2.7 39.5 1.0
OD2 A:ASP295 2.8 26.0 1.0
O A:HOH627 2.8 28.1 0.9
O A:GLU290 2.9 25.7 1.0
HA A:PHE291 2.9 30.3 1.0
HG1 A:THR111 3.1 32.6 1.0
HG23 A:THR111 3.2 33.6 1.0
NE2 A:GLN127 3.3 30.4 1.0
HD1 A:PHE291 3.3 39.0 1.0
HB A:THR111 3.4 34.6 1.0
CG A:ASP295 3.4 32.7 1.0
CG A:GLN127 3.4 32.9 1.0
HG3 A:GLN127 3.5 39.5 1.0
HB3 A:ASP295 3.6 33.9 1.0
CD1 A:PHE291 3.7 32.4 1.0
OG1 A:THR111 3.8 27.1 1.0
CB A:THR111 3.8 28.7 1.0
CD A:GLN127 3.8 27.9 1.0
CG2 A:THR111 3.9 27.9 1.0
CA A:PHE291 3.9 25.1 1.0
HE22 A:GLN127 3.9 36.6 1.0
CB A:ASP295 4.0 28.1 1.0
C A:GLU290 4.0 33.9 1.0
H A:THR292 4.0 27.9 1.0
OD1 A:ASP295 4.1 30.3 1.0
HB2 A:ASP295 4.1 33.9 1.0
HG21 A:THR111 4.1 33.6 1.0
HE1 A:PHE291 4.2 29.5 1.0
CE1 A:PHE291 4.2 24.5 1.0
CG A:PHE291 4.3 21.2 1.0
N A:PHE291 4.4 22.9 1.0
CB A:PHE291 4.6 24.1 1.0
HG3 A:LYS5 4.6 34.0 0.6
O A:HOH557 4.6 30.3 1.0
N A:THR292 4.7 23.2 1.0
HG22 A:THR111 4.7 33.6 1.0
HH11 A:ARG298 4.7 35.5 1.0
CB A:GLN127 4.7 30.5 1.0
O A:HOH654 4.7 25.8 0.8
HB3 A:GLN127 4.7 36.8 1.0
HB3 A:PHE291 4.8 29.1 1.0
HE2 A:LYS5 4.8 44.2 0.6
HG21 A:THR292 4.8 32.3 1.0
C A:PHE291 4.8 23.9 1.0
O A:MET6 4.9 30.6 1.0
H A:MET6 4.9 38.6 1.0
HB3 A:GLU290 4.9 28.4 1.0

Reference:

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
Page generated: Sun Jan 24 12:02:51 2021

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