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Zinc in PDB 4f5c: Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain

Enzymatic activity of Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain

All present enzymatic activity of Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain:
3.4.11.2;

Protein crystallography data

The structure of Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain, PDB code: 4f5c was solved by C.Santiago, J.Reguera, M.Gaurav, D.Ordono, L.Enjuanes, J.M.Casasnovas, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 24.91 / 3.20
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 220.859, 87.938, 176.912, 90.00, 90.54, 90.00
R / Rfree (%) 20.1 / 24.5

Zinc Binding Sites:

The binding sites of Zinc atom in the Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain (pdb code 4f5c). 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 the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain, PDB code: 4f5c:
Jump to Zinc binding site number: 1; 2;

Zinc binding site 1 out of 2 in 4f5c

Go back to Zinc Binding Sites List in 4f5c
Zinc binding site 1 out of 2 in the Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain


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 the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Zn1001

b:75.2
occ:1.00
OE1 A:GLU406 2.0 51.8 1.0
NE2 A:HIS383 2.0 31.3 1.0
OE2 A:GLU406 2.0 67.1 1.0
NE2 A:HIS387 2.0 86.0 1.0
O A:HOH1101 2.1 49.1 1.0
CD A:GLU406 2.2 59.8 1.0
CE1 A:HIS387 2.8 87.8 1.0
CE1 A:HIS383 2.9 60.0 1.0
CD2 A:HIS387 2.9 80.6 1.0
CD2 A:HIS383 3.0 54.1 1.0
CG A:GLU406 3.8 60.4 1.0
ND1 A:HIS387 3.8 81.3 1.0
OE2 A:GLU384 3.8 72.7 1.0
CG A:HIS387 3.9 81.8 1.0
O A:HOH1102 4.0 71.4 1.0
ND1 A:HIS383 4.0 52.0 1.0
CG A:HIS383 4.1 46.9 1.0
OE1 A:GLU350 4.4 0.7 1.0
OE2 A:GLU350 4.5 0.4 1.0
CA A:GLU406 4.5 60.0 1.0
CB A:GLU406 4.5 55.2 1.0
CD A:GLU384 4.6 71.1 1.0
CD A:GLU350 4.6 0.5 1.0
OH A:TYR472 4.6 75.2 1.0
CB A:ALA409 4.6 64.6 1.0
OE1 A:GLU384 4.6 76.3 1.0

Zinc binding site 2 out of 2 in 4f5c

Go back to Zinc Binding Sites List in 4f5c
Zinc binding site 2 out of 2 in the Crystal Structure of the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain


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 the Spike Receptor Binding Domain of A Porcine Respiratory Coronavirus in Complex with the Pig Aminopeptidase N Ectodomain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Zn1001

b:83.0
occ:1.00
NE2 B:HIS383 1.9 41.5 1.0
OE1 B:GLU406 2.0 48.9 1.0
OE2 B:GLU406 2.0 66.6 1.0
NE2 B:HIS387 2.1 83.2 1.0
O B:HOH1101 2.1 78.3 1.0
CD B:GLU406 2.3 58.5 1.0
CE1 B:HIS387 2.8 85.3 1.0
CE1 B:HIS383 2.9 59.8 1.0
CD2 B:HIS387 2.9 76.1 1.0
CD2 B:HIS383 3.0 56.2 1.0
OE1 B:GLU350 3.7 68.2 1.0
OE2 B:GLU384 3.8 73.7 1.0
CG B:GLU406 3.8 64.0 1.0
ND1 B:HIS387 3.8 79.8 1.0
O B:HOH1102 3.9 63.3 1.0
CG B:HIS387 3.9 77.0 1.0
ND1 B:HIS383 4.0 50.4 1.0
OE2 B:GLU350 4.1 84.6 1.0
CG B:HIS383 4.1 49.9 1.0
CD B:GLU350 4.1 77.2 1.0
CD B:GLU384 4.5 72.4 1.0
OH B:TYR472 4.5 69.8 1.0
OE1 B:GLU384 4.5 75.7 1.0
CB B:ALA409 4.6 62.4 1.0
CB B:GLU406 4.6 55.3 1.0
CA B:GLU406 4.6 63.9 1.0

Reference:

J.Reguera, C.Santiago, G.Mudgal, D.Ordono, L.Enjuanes, J.M.Casasnovas. Structural Bases of Coronavirus Attachment to Host Aminopeptidase N and Its Inhibition By Neutralizing Antibodies. Plos Pathog. V. 8 02859 2012.
ISSN: ISSN 1553-7366
PubMed: 22876187
DOI: 10.1371/JOURNAL.PPAT.1002859
Page generated: Wed Dec 16 05:16:56 2020

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