Zinc in PDB 7rpv: Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd

The structure of Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd, PDB code: 7rpv was solved by Y.Chen, D.W.Tolbert, M.Pazgier, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	47.92 / 3.54
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	132.666, 136.307, 132.673, 90, 92.51, 90
R / Rfree (%)	24.4 / 29.2

The binding sites of Zinc atom in the Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd (pdb code 7rpv). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd, PDB code: 7rpv:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd


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 Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn1007 b:142.3 occ:1.00 OH A:TYR515 2.7 127.9 1.0 CE1 A:HIS345 3.1 142.8 1.0 NH2 A:ARG273 3.3 104.5 1.0 NE2 A:HIS345 3.3 143.4 1.0 CZ A:TYR515 3.6 130.0 1.0 CE2 A:TYR515 3.8 129.7 1.0 NE2 A:HIS505 3.8 115.0 1.0 CE1 A:HIS505 3.9 110.0 1.0 CZ A:ARG273 4.3 115.7 1.0 ND1 A:HIS345 4.4 143.1 1.0 NH1 A:ARG273 4.5 125.8 1.0 CD2 A:HIS345 4.6 144.3 1.0 CE1 A:TYR515 4.7 119.5 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd


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 Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn1007 b:103.2 occ:1.00 OH B:TYR515 2.5 113.2 1.0 CZ B:TYR515 3.4 114.4 1.0 NE2 B:HIS345 3.7 135.9 1.0 NE2 B:HIS505 3.9 112.9 1.0 CE1 B:HIS345 3.9 139.4 1.0 NH1 B:ARG273 4.0 104.7 1.0 CE1 B:TYR515 4.1 112.0 1.0 NH2 B:ARG273 4.1 109.5 1.0 CE2 B:TYR515 4.3 106.7 1.0 CE1 B:HIS505 4.3 106.3 1.0 CZ B:ARG273 4.5 102.5 1.0 CD2 B:HIS345 4.8 132.4 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn1007 b:115.6 occ:1.00 OH C:TYR515 3.2 126.2 1.0 CE1 C:HIS505 3.8 123.7 1.0 NE2 C:HIS505 3.9 123.7 1.0 NE2 C:HIS345 3.9 129.2 1.0 CZ C:TYR515 4.1 101.2 1.0 NH1 C:ARG273 4.1 86.7 1.0 NH2 C:ARG273 4.4 85.9 1.0 CE1 C:HIS345 4.4 132.3 1.0 CE1 C:TYR515 4.4 96.8 1.0 CZ C:ARG273 4.7 89.5 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Affinity-Enhancing and Catalytically Inactive ACE2 in Complex with Sars-Cov-2 Rbd within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn1007 b:112.1 occ:1.00 OH D:TYR515 2.9 111.5 1.0 NH2 D:ARG273 3.8 96.8 1.0 NE2 D:HIS345 3.8 134.9 1.0 CZ D:TYR515 3.9 92.7 1.0 CE1 D:HIS345 4.1 137.8 1.0 NE2 D:HIS505 4.2 99.1 1.0 CE2 D:TYR515 4.3 88.8 1.0 CE1 D:HIS505 4.5 106.4 1.0 NH1 D:ARG273 4.6 103.5 1.0 CZ D:ARG273 4.7 85.5 1.0 CD2 D:HIS345 5.0 118.1 1.0 NH2 D:ARG518 5.0 114.0 1.0 CE1 D:TYR515 5.0 82.8 1.0

Y.Chen, L.Sun, I.Ullah, G.Beaudoin-Bussieres, S.P.Anand, A.P.Hederman, W.D.Tolbert, R.Sherburn, D.N.Nguyen, L.Marchitto, S.Ding, D.Wu, Y.Luo, S.Gottumukkala, S.Moran, P.Kumar, G.Piszczek, W.Mothes, M.E.Ackerman, A.Finzi, P.D.Uchil, F.J.Gonzalez, M.Pazgier. Engineered ACE2-Fc Counters Murine Lethal Sars-Cov-2 Infection Through Direct Neutralization and Fc-Effector Activities. Biorxiv 2021.
PubMed: 34845451
DOI: 10.1101/2021.11.24.469776