Sodium in PDB 4adi: Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I)

The structure of Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I), PDB code: 4adi was solved by R.M.Dubois, M.C.Vaney, M.A.Tortorici, R.Al Kurdi, G.Barba-Spaeth, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	20.00 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	129.980, 121.380, 126.430, 90.00, 90.00, 90.00
R / Rfree (%)	16.66 / 18.31

The binding sites of Sodium atom in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I) (pdb code 4adi). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 3 binding sites of Sodium where determined in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I), PDB code: 4adi:
Jump to Sodium binding site number: 1; 2; 3;

Sodium binding site 1 out of 3 in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I)


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 the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1442 b:31.9 occ:1.00 O A:ALA89 2.2 23.3 1.0 OD2 A:ASP136 2.2 50.4 1.0 OD1 A:ASN88 2.3 29.2 1.0 O A:THR137 2.4 27.5 1.0 O A:HOH2174 2.5 37.0 1.0 CG A:ASN88 3.2 37.0 1.0 CG A:ASP136 3.3 50.8 1.0 C A:ALA89 3.5 24.7 1.0 C A:THR137 3.6 28.7 1.0 CB A:ASP136 3.8 38.7 1.0 ND2 A:ASN88 3.9 27.4 1.0 C A:ASN88 4.0 23.4 1.0 N A:ALA89 4.0 21.0 1.0 CB A:ASN88 4.1 20.1 1.0 O A:ASN88 4.2 22.3 1.0 N A:SER91 4.2 25.0 1.0 CG2 A:VAL138 4.2 27.5 1.0 N A:THR137 4.3 29.9 1.0 CA A:ALA89 4.4 21.2 1.0 N A:TYR90 4.4 22.1 1.0 N A:VAL138 4.4 24.0 1.0 CA A:VAL138 4.4 23.1 1.0 C A:ASP136 4.4 35.7 1.0 C A:TYR90 4.4 27.2 1.0 OD1 A:ASP136 4.4 58.9 1.0 O A:HOH2073 4.4 48.5 1.0 CA A:TYR90 4.5 22.1 1.0 CA A:ASN88 4.5 19.9 1.0 O A:ACT1443 4.5 59.4 1.0 O A:HOH2173 4.6 29.0 1.0 CA A:THR137 4.6 28.2 1.0 O A:ASP136 4.7 34.9 1.0 CB A:SER91 4.7 28.1 1.0 CA A:ASP136 4.7 36.4 1.0 CA A:SER91 4.9 25.1 1.0 CB A:VAL138 4.9 27.4 1.0

Sodium binding site 2 out of 3 in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I)


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 the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na1439 b:30.0 occ:1.00 OD2 B:ASP136 2.2 47.5 1.0 O B:ALA89 2.2 24.1 1.0 OD1 B:ASN88 2.3 30.1 1.0 O B:THR137 2.4 29.6 1.0 O B:HOH2132 2.5 41.3 1.0 CG B:ASN88 3.2 37.4 1.0 CG B:ASP136 3.3 48.7 1.0 C B:ALA89 3.5 25.0 1.0 C B:THR137 3.6 30.9 1.0 CB B:ASP136 3.8 38.9 1.0 ND2 B:ASN88 3.9 29.7 1.0 C B:ASN88 4.0 23.8 1.0 O B:HOH2138 4.0 39.7 1.0 N B:ALA89 4.1 21.4 1.0 CB B:ASN88 4.1 20.5 1.0 O B:ASN88 4.2 22.9 1.0 N B:SER91 4.2 23.9 1.0 CG2 B:VAL138 4.2 29.6 1.0 N B:THR137 4.3 32.1 1.0 CA B:ALA89 4.4 21.6 1.0 N B:TYR90 4.4 21.4 1.0 N B:VAL138 4.4 25.4 1.0 C B:ASP136 4.4 37.4 1.0 CA B:VAL138 4.4 24.5 1.0 C B:TYR90 4.4 25.4 1.0 OD1 B:ASP136 4.4 55.3 1.0 CA B:TYR90 4.5 21.6 1.0 CA B:ASN88 4.5 19.8 1.0 O B:HOH2131 4.6 29.2 1.0 O B:HOH2047 4.6 44.5 1.0 CA B:THR137 4.6 30.6 1.0 O B:ASP136 4.7 36.5 1.0 CB B:SER91 4.7 27.8 1.0 CA B:ASP136 4.8 37.2 1.0 CA B:SER91 4.9 24.3 1.0 CB B:VAL138 4.9 29.3 1.0 O B:HOH2134 5.0 43.2 1.0

Sodium binding site 3 out of 3 in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form I) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1443 b:32.2 occ:1.00 OD2 C:ASP136 2.2 53.2 1.0 O C:ALA89 2.2 22.7 1.0 O C:HOH2127 2.3 40.7 1.0 OD1 C:ASN88 2.3 30.4 1.0 O C:THR137 2.5 27.7 1.0 CG C:ASN88 3.2 37.0 1.0 CG C:ASP136 3.3 49.7 1.0 C C:ALA89 3.5 23.6 1.0 C C:THR137 3.6 29.0 1.0 CB C:ASP136 3.8 39.3 1.0 ND2 C:ASN88 3.8 29.9 1.0 C C:ASN88 4.0 22.2 1.0 N C:ALA89 4.1 20.0 1.0 CB C:ASN88 4.1 19.4 1.0 N C:SER91 4.2 23.5 1.0 CG2 C:VAL138 4.2 25.2 1.0 O C:ASN88 4.2 21.1 1.0 N C:THR137 4.3 31.4 1.0 CA C:ALA89 4.4 19.9 1.0 C C:TYR90 4.4 25.5 1.0 N C:TYR90 4.4 20.3 1.0 OD1 C:ASP136 4.4 51.1 1.0 C C:ASP136 4.4 37.1 1.0 O C:ACT1444 4.4 56.5 1.0 CA C:TYR90 4.4 20.5 1.0 N C:VAL138 4.5 23.0 1.0 CA C:VAL138 4.5 21.4 1.0 CA C:ASN88 4.5 18.6 1.0 O C:HOH2044 4.6 43.6 1.0 O C:HOH2126 4.6 27.9 1.0 CA C:THR137 4.6 29.9 1.0 CB C:SER91 4.7 27.7 1.0 O C:ASP136 4.8 36.0 1.0 CA C:ASP136 4.8 37.3 1.0 CA C:SER91 4.8 24.0 1.0 O C:HOH2128 4.9 45.9 1.0 CB C:VAL138 4.9 25.4 1.0

R.M.Dubois, M.C.Vaney, M.A.Tortorici, R.A.Kurdi, G.Barba-Spaeth, T.Krey, F.A.Rey. Functional and Evolutionary Insight From the Crystal Structure of Rubella Virus Protein E1. Nature V. 493 552 2013.
ISSN: ISSN 0028-0836
PubMed: 23292515
DOI: 10.1038/NATURE11741