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Sodium in PDB 5jil: Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid

Enzymatic activity of Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid

All present enzymatic activity of Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid:
3.1.1.53;

Protein crystallography data

The structure of Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid, PDB code: 5jil was solved by M.J.G.Bakkers, L.J.Feitsma, R.J.De Groot, E.G.Huizinga, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 92.29 / 1.85
Space group C 2 2 21
Cell size a, b, c (Å), α, β, γ (°) 57.090, 184.590, 78.080, 90.00, 90.00, 90.00
R / Rfree (%) 18.4 / 20

Other elements in 5jil:

The structure of Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid also contains other interesting chemical elements:

Zinc (Zn) 1 atom

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid (pdb code 5jil). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid, PDB code: 5jil:

Sodium binding site 1 out of 1 in 5jil

Go back to Sodium Binding Sites List in 5jil
Sodium binding site 1 out of 1 in the Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Rat Coronavirus Strain New-Jersey Hemagglutinin- Esterase in Complex with 4N-Acetyl Sialic Acid within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na510

b:27.2
occ:1.00
 OD1 A:ASP225 2.4 23.3 1.0
OG A:SER273 2.4 22.3 1.0
O A:LEU277 2.5 21.2 1.0
O A:SER226 2.6 23.7 1.0
O A:GLU275 2.7 23.3 1.0
OE1 A:GLN227 3.4 23.9 1.0
CB A:SER273 3.4 22.4 1.0
C A:LEU277 3.5 22.0 1.0
C A:SER226 3.6 23.6 1.0
CG A:ASP225 3.6 23.1 1.0
N A:SER226 3.7 24.1 1.0
O A:HOH608 3.7 42.7 1.0
C A:GLU275 3.9 24.0 1.0
N A:LEU277 3.9 22.7 1.0
O A:HOH681 3.9 32.9 1.0
C A:PHE276 4.0 23.4 1.0
CA A:SER273 4.1 22.6 1.0
OD2 A:ASP225 4.2 22.3 1.0
CA A:SER226 4.3 24.0 1.0
N A:LEU278 4.3 22.0 1.0
O A:PHE276 4.3 23.7 1.0
CA A:LEU277 4.4 22.7 1.0
CB A:GLN227 4.5 22.4 1.0
CD A:GLN227 4.5 23.3 1.0
N A:GLN227 4.5 22.9 1.0
CA A:LEU278 4.5 21.6 1.0
CB A:PHE276 4.5 23.2 1.0
CA A:PHE276 4.6 23.8 1.0
C A:ASP225 4.6 24.2 1.0
N A:GLU275 4.6 24.4 1.0
CA A:ASP225 4.6 24.6 1.0
CA A:GLN227 4.6 22.7 1.0
N A:PHE276 4.7 24.3 1.0
CB A:ASP225 4.7 23.7 1.0
O A:HOH639 4.7 19.4 1.0
C A:SER273 4.8 23.4 1.0
N A:LEU274 4.9 23.7 1.0
CA A:GLU275 4.9 24.9 1.0

Reference:

M.J.Bakkers, Q.Zeng, L.J.Feitsma, R.J.Hulswit, Z.Li, A.Westerbeke, F.J.Van Kuppeveld, G.J.Boons, M.A.Langereis, E.G.Huizinga, R.J.De Groot. Coronavirus Receptor Switch Explained From the Stereochemistry of Protein-Carbohydrate Interactions and A Single Mutation. Proc.Natl.Acad.Sci.Usa V. 113 E3111 2016.
ISSN: ESSN 1091-6490
PubMed: 27185912
DOI: 10.1073/PNAS.1519881113
Page generated: Mon Aug 18 00:31:33 2025

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