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Sodium in PDB 5jif: Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase

Enzymatic activity of Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase

All present enzymatic activity of Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase:
3.1.1.53;

Protein crystallography data

The structure of Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase, PDB code: 5jif was solved by Q.H.Zeng, 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) 39.73 / 2.00
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 88.523, 88.819, 122.163, 90.00, 90.00, 90.00
R / Rfree (%) 20.5 / 22.6

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase (pdb code 5jif). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase, PDB code: 5jif:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 5jif

Go back to Sodium Binding Sites List in 5jif
Sodium binding site 1 out of 2 in the Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase


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 Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na801

b:43.4
occ:1.00
O A:LEU275 2.2 43.8 1.0
O A:HOH963 2.2 42.9 1.0
O A:SER229 2.4 41.3 1.0
OE1 A:GLN230 2.6 40.1 1.0
OD1 A:ASP228 2.6 49.6 1.0
C A:SER229 3.3 41.6 1.0
C A:LEU275 3.4 47.7 1.0
CG A:ASP228 3.5 47.7 1.0
CD A:GLN230 3.5 39.4 1.0
CB A:GLN230 3.6 37.4 1.0
OD2 A:ASP228 3.8 49.7 1.0
CB A:SER271 3.8 44.2 1.0
N A:SER229 3.9 43.8 1.0
CG A:GLN230 4.0 38.0 1.0
OG1 A:THR277 4.0 48.0 1.0
CA A:GLN230 4.0 38.7 1.0
N A:GLN230 4.0 39.1 1.0
N A:THR277 4.2 44.8 1.0
CA A:SER229 4.3 43.0 1.0
CA A:LEU275 4.3 47.8 1.0
N A:LEU276 4.4 46.6 1.0
CA A:LEU276 4.4 45.8 1.0
CB A:LEU275 4.5 48.0 1.0
N A:LEU275 4.5 47.3 1.0
C A:LEU276 4.6 44.4 1.0
CA A:SER271 4.6 44.5 1.0
CG2 A:THR277 4.7 45.9 1.0
NE2 A:GLN230 4.7 40.7 1.0
O A:CYS213 4.7 43.1 1.0
CG1 A:VAL214 4.8 43.2 1.0
CB A:THR277 4.8 44.4 1.0
OG A:SER271 4.9 46.4 1.0
CB A:ASP228 4.9 45.0 1.0
CG A:LEU275 5.0 49.6 1.0

Sodium binding site 2 out of 2 in 5jif

Go back to Sodium Binding Sites List in 5jif
Sodium binding site 2 out of 2 in the Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Mouse Hepatitis Virus Strain Dvim Hemagglutinin- Esterase within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na801

b:51.0
occ:1.00
O B:LEU275 2.2 48.1 1.0
O B:SER229 2.3 45.8 1.0
O B:HOH961 2.4 46.6 1.0
OE1 B:GLN230 2.5 46.0 1.0
OD1 B:ASP228 2.6 51.3 1.0
C B:SER229 3.3 45.5 1.0
C B:LEU275 3.4 52.5 1.0
CD B:GLN230 3.5 47.2 1.0
CG B:ASP228 3.5 52.6 1.0
CB B:GLN230 3.6 42.2 1.0
CB B:SER271 3.7 47.2 1.0
OD2 B:ASP228 3.8 52.6 1.0
N B:SER229 4.0 48.0 1.0
CA B:GLN230 4.0 42.6 1.0
CG B:GLN230 4.0 44.1 1.0
N B:GLN230 4.0 42.8 1.0
OG1 B:THR277 4.0 49.3 1.0
N B:THR277 4.1 47.4 1.0
CA B:LEU275 4.3 54.5 1.0
CA B:SER229 4.3 45.6 1.0
N B:LEU276 4.3 50.1 1.0
CA B:LEU276 4.3 49.8 1.0
CB B:LEU275 4.5 57.7 1.0
N B:LEU275 4.5 54.5 1.0
CA B:SER271 4.5 46.7 1.0
C B:LEU276 4.6 49.1 1.0
NE2 B:GLN230 4.6 48.5 1.0
CG2 B:THR277 4.7 52.4 1.0
O B:CYS213 4.7 41.2 1.0
OG B:SER271 4.8 49.9 1.0
CB B:THR277 4.8 49.6 1.0
CG1 B:VAL214 4.9 49.0 1.0
CB B:ASP228 4.9 51.1 1.0
C B:LEU274 4.9 53.7 1.0
CG B:LEU275 5.0 57.5 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: Tue Dec 15 11:08:13 2020

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