Zinc in PDB 7p19: Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2

The structure of Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2, PDB code: 7p19 was solved by E.Erausquin, J.Lopez-Sagaseta, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	93.99 / 3.24
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	60.591, 165.037, 228.678, 90, 90, 90
R / Rfree (%)	23.1 / 28.9

The structure of Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2 also contains other interesting chemical elements:

Chlorine

(Cl)

1 atom

The binding sites of Zinc atom in the Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2 (pdb code 7p19). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2, PDB code: 7p19:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in the Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn702 b:91.3 occ:1.00 OE2 A:GLU402 2.0 61.8 1.0 NE2 A:HIS374 2.3 59.6 1.0 NE2 A:HIS378 2.3 76.2 1.0 CD2 A:HIS378 2.9 81.3 1.0 CD A:GLU402 3.0 65.8 1.0 CD2 A:HIS374 3.1 75.7 1.0 OE2 A:GLU375 3.2 84.5 1.0 OE1 A:GLU402 3.3 68.8 1.0 CE1 A:HIS374 3.4 80.2 1.0 CE1 A:HIS378 3.4 72.7 1.0 CG A:HIS378 4.1 78.6 1.0 CG A:GLU402 4.3 69.4 1.0 CD A:GLU375 4.3 87.3 1.0 ND1 A:HIS378 4.3 72.3 1.0 CG A:HIS374 4.3 79.0 1.0 ND1 A:HIS374 4.4 82.0 1.0 OE1 A:GLU375 4.8 101.4 1.0

Zinc binding site 2 out of 2 in the Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Sars-Cov-2 Rbd Q498Y Complexed with Human ACE2 within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn702 b:100.7 occ:1.00 OE2 B:GLU402 2.0 82.2 1.0 NE2 B:HIS374 2.3 91.2 1.0 NE2 B:HIS378 2.3 95.7 1.0 CD2 B:HIS378 2.9 95.3 1.0 CD B:GLU402 3.0 80.9 1.0 CD2 B:HIS374 3.1 95.2 1.0 OE2 B:GLU375 3.2 109.8 1.0 CE1 B:HIS374 3.4 93.0 1.0 CE1 B:HIS378 3.4 84.7 1.0 OE1 B:GLU402 3.4 89.3 1.0 CG B:HIS378 4.1 87.7 1.0 CD B:GLU375 4.2 107.0 1.0 ND1 B:HIS378 4.3 83.0 1.0 CG B:GLU402 4.3 82.2 1.0 CG B:HIS374 4.3 103.4 1.0 ND1 B:HIS374 4.4 100.2 1.0 OE1 B:GLU375 4.7 115.1 1.0

E.Erausquin, F.Glaser, J.Fernandez-Recio, J.Lopez-Sagaseta. Structural Bases For the Higher Adherence to ACE2 Conferred By the Sars-Cov-2 Spike Q498Y Substitution. Acta Crystallogr D Struct V. 78 1156 2022BIOL.
ISSN: ISSN 2059-7983
PubMed: 36048155
DOI: 10.1107/S2059798322007677