Zinc in PDB 7vpp: Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans

Protein crystallography data

The structure of Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans, PDB code: 7vpp was solved by W.Ji, Y.Xu, S.Zhang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 42.65 / 2.69
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 186.643, 186.643, 173.823, 90, 90, 90
R / Rfree (%) 19.8 / 23

Zinc Binding Sites:

The binding sites of Zinc atom in the Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans (pdb code 7vpp). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 2 binding sites of Zinc where determined in the Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans, PDB code: 7vpp:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 7vpp

Go back to Zinc Binding Sites List in 7vpp
Zinc binding site 1 out of 2 in the Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:49.3
occ:1.00
OE1 A:GLU406 1.9 48.9 1.0
NE2 A:HIS387 2.3 40.7 1.0
NE2 A:HIS383 2.3 43.9 1.0
O A:HOH1118 2.4 41.2 1.0
CD A:GLU406 2.6 56.2 1.0
OE2 A:GLU406 2.7 59.9 1.0
CD2 A:HIS387 3.0 42.3 1.0
CD2 A:HIS383 3.1 49.7 1.0
CE1 A:HIS383 3.4 58.2 1.0
CE1 A:HIS387 3.4 51.6 1.0
OH A:TYR472 3.6 51.9 1.0
CE2 A:TYR472 3.9 47.8 1.0
OE1 A:GLU350 4.0 59.0 1.0
CG A:GLU406 4.1 47.6 1.0
CZ A:TYR472 4.1 51.5 1.0
CG A:HIS387 4.3 53.7 1.0
CG A:HIS383 4.3 48.9 1.0
CB A:ALA409 4.3 37.5 1.0
ND1 A:HIS387 4.4 47.3 1.0
ND1 A:HIS383 4.4 47.1 1.0
CB A:GLU406 4.6 50.5 1.0
CA A:GLU406 4.7 49.8 1.0
OE2 A:GLU384 4.7 54.8 1.0
CD A:GLU350 4.8 59.7 1.0
OE1 A:GLU384 5.0 65.7 1.0
CD2 A:TYR472 5.0 51.5 1.0

Zinc binding site 2 out of 2 in 7vpp

Go back to Zinc Binding Sites List in 7vpp
Zinc binding site 2 out of 2 in the Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors Indicate the Risk of Virus Adaptation to Humans within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Zn1001

b:54.5
occ:1.00
OE1 C:GLU406 1.9 51.1 1.0
NE2 C:HIS387 2.3 46.0 1.0
O C:HOH1116 2.3 44.1 1.0
NE2 C:HIS383 2.3 46.4 1.0
CD C:GLU406 2.7 63.9 1.0
OE2 C:GLU406 2.9 64.8 1.0
CD2 C:HIS387 2.9 48.2 1.0
CD2 C:HIS383 3.0 52.8 1.0
CE1 C:HIS383 3.5 59.5 1.0
CE1 C:HIS387 3.5 62.1 1.0
OE1 C:GLU350 3.9 78.8 1.0
OH C:TYR472 4.0 53.6 1.0
CE2 C:TYR472 4.0 50.1 1.0
CG C:GLU406 4.2 45.7 1.0
CG C:HIS387 4.2 51.3 1.0
CG C:HIS383 4.2 45.4 1.0
CB C:ALA409 4.4 47.9 1.0
CZ C:TYR472 4.4 53.3 1.0
ND1 C:HIS387 4.4 52.4 1.0
ND1 C:HIS383 4.4 49.2 1.0
OE2 C:GLU384 4.6 71.2 1.0
CB C:GLU406 4.7 45.6 1.0
CA C:GLU406 4.7 53.7 1.0
CD C:GLU350 4.7 60.2 1.0
OE2 C:GLU350 4.9 63.1 1.0

Reference:

W.Ji, Q.Peng, X.Fang, Z.Li, Y.Li, C.Xu, S.Zhao, J.Li, R.Chen, G.Mo, Z.Wei, Y.Xu, B.Li, S.Zhang. Structures of A Deltacoronavirus Spike Protein Bound to Porcine and Human Receptors. Nat Commun V. 13 1467 2022.
ISSN: ESSN 2041-1723
PubMed: 35304871
DOI: 10.1038/S41467-022-29062-5
Page generated: Sat Apr 8 04:46:19 2023

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