Sodium in PDB 7a56: Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation

The structure of Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation, PDB code: 7a56 was solved by J.Hellert, P.Guardado-Calvo, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.41 / 1.85
Space group	H 3 2
Cell size a, b, c (Å), α, β, γ (°)	86.79, 86.79, 358.09, 90, 90, 120
R / Rfree (%)	17 / 20.9

The structure of Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation also contains other interesting chemical elements:

Potassium	(K)	1 atom
Chlorine	(Cl)	6 atoms

The binding sites of Sodium atom in the Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation (pdb code 7a56). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation, PDB code: 7a56:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1410 b:75.8 occ:1.00 O A:HOH1917 2.5 70.1 1.0 CG A:TYR911 3.8 51.0 1.0 CD1 A:TYR911 3.8 56.1 1.0 CD2 A:TYR911 4.0 55.2 1.0 CE1 A:TYR911 4.1 60.8 1.0 CE2 A:TYR911 4.3 59.7 1.0 CZ A:TYR911 4.3 63.5 1.0 CB A:TYR911 4.4 43.0 1.0

Sodium binding site 2 out of 4 in the Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1411 b:62.2 occ:1.00 O A:HOH1715 3.4 33.0 1.0 CZ2 A:TRP1029 3.4 39.8 1.0 CE2 A:TRP1029 3.6 36.8 1.0 CB A:ALA1157 3.7 38.0 1.0 CH2 A:TRP1029 3.8 46.9 1.0 CA A:GLY1030 4.0 30.3 1.0 NE1 A:TRP1029 4.1 37.6 1.0 N A:GLY1030 4.1 32.7 1.0 CD2 A:TRP1029 4.2 34.9 1.0 CZ3 A:TRP1029 4.3 44.0 1.0 CE3 A:TRP1029 4.5 37.6 1.0 CA A:ALA1157 4.6 33.8 1.0 CD1 A:TRP1029 4.8 34.2 1.0 CG A:TRP1029 4.9 31.8 1.0

Sodium binding site 3 out of 4 in the Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1412 b:61.2 occ:1.00 CE2 A:TRP1034 4.0 62.8 1.0 CD2 A:TRP1034 4.1 60.2 1.0 NE1 A:TRP1034 4.2 59.8 1.0 CZ2 A:TRP1034 4.3 69.0 1.0 CG A:TRP1034 4.4 55.4 1.0 CD1 A:TRP1034 4.5 55.2 1.0 CE3 A:TRP1034 4.5 63.8 1.0 CH2 A:TRP1034 4.7 74.9 1.0 CZ3 A:TRP1034 4.8 68.4 1.0

Sodium binding site 4 out of 4 in the Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Schmallenberg Virus Envelope Glycoprotein Gc Fusion Domains in Postfusion Conformation within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1413 b:62.8 occ:1.00 O A:HOH1686 3.8 59.9 1.0 CE2 A:TYR1219 4.0 33.1 1.0 CZ A:TYR1219 4.0 32.7 1.0 CD2 A:TYR1219 4.1 33.0 1.0 CE1 A:TYR1219 4.1 30.4 1.0 CG A:TYR1219 4.3 31.8 1.0 CD1 A:TYR1219 4.3 28.8 1.0 OH A:TYR1219 4.5 33.8 1.0 O A:HOH1858 4.8 40.1 1.0 O A:HOH1716 4.8 55.4 1.0 OD1 A:ASN959 4.9 47.6 1.0

J.Hellert, A.Aebischer, A.Haouz, P.Guardado-Calvo, S.Reiche, M.Beer, F.A.Rey. Structure, Function and Evolution of the Orthobunyavirus Envelope Glycoprotein Gc Core Fragment To Be Published.