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

Protein crystallography data

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

Zinc Binding Sites:

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 7rpv

Go back to Zinc Binding Sites List in 7rpv
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 7rpv

Go back to Zinc Binding Sites List in 7rpv
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 7rpv

Go back to Zinc Binding Sites List in 7rpv
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 7rpv

Go back to Zinc Binding Sites List in 7rpv
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

Reference:

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
Page generated: Fri Dec 17 11:55:05 2021

Last articles

Cd in 3P5X
Cd in 3PV4
Cd in 3PO0
Cd in 3PNR
Cd in 3OEO
Cd in 3P5V
Cd in 3P5W
Cd in 3P5U
Cd in 3OW2
Cd in 3OVN
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy