Sodium in PDB 4adj: Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate

The structure of Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate, PDB code: 4adj 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)	38.80 / 1.94
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	121.875, 126.899, 130.946, 90.00, 90.00, 90.00
R / Rfree (%)	18.19 / 19.4

The structure of Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate also contains other interesting chemical elements:

Calcium

(Ca)

3 atoms

The binding sites of Sodium atom in the Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate (pdb code 4adj). 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 the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate, PDB code: 4adj:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate


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 Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate within 5.0Å range: probe atom residue distance (Å) B Occ A:Na1439 b:26.9 occ:0.45 CA A:CA1440 0.5 55.7 0.6 O A:HOH2114 2.1 45.8 1.0 O A:ALA89 2.2 37.1 1.0 OD1 A:ASN88 2.3 40.9 1.0 OD2 A:ASP136 2.3 56.0 0.5 O A:THR137 2.5 39.1 0.5 OD1 A:ASP136 2.5 50.7 0.5 O A:THR137 2.6 39.6 0.5 CG A:ASN88 3.3 50.2 1.0 CG A:ASP136 3.3 55.7 0.5 C A:ALA89 3.5 38.0 1.0 C A:THR137 3.7 39.7 0.5 CG A:ASP136 3.7 50.9 0.5 CB A:ASP136 3.7 44.3 0.5 C A:THR137 3.8 39.9 0.5 ND2 A:ASN88 4.0 41.2 1.0 N A:SER91 4.1 38.8 1.0 N A:ALA89 4.1 33.7 1.0 C A:ASN88 4.1 36.2 1.0 N A:THR137 4.2 38.9 0.5 OD2 A:ASP136 4.2 56.4 0.5 CB A:ASN88 4.3 33.0 1.0 CG1 A:VAL138 4.3 38.2 0.5 O A:HOH2042 4.3 62.2 1.0 C A:TYR90 4.3 41.3 1.0 N A:TYR90 4.4 35.4 1.0 O A:ASN88 4.4 35.6 1.0 N A:THR137 4.4 38.6 0.5 CA A:ALA89 4.4 33.9 1.0 CG2 A:VAL138 4.4 38.7 0.5 OD1 A:ASP136 4.4 63.0 0.5 CA A:TYR90 4.4 35.8 1.0 C A:ASP136 4.5 43.6 0.5 O A:HOH2113 4.5 44.1 1.0 CA A:THR137 4.5 37.9 0.5 CB A:SER91 4.6 43.0 1.0 N A:VAL138 4.6 35.0 0.5 C A:ASP136 4.6 43.6 0.5 N A:VAL138 4.6 35.4 0.5 CA A:ASN88 4.6 32.2 1.0 CA A:VAL138 4.6 34.5 0.5 CA A:VAL138 4.7 34.1 0.5 CA A:SER91 4.7 39.7 1.0 CA A:ASP136 4.8 42.2 0.5 CA A:THR137 4.8 37.4 0.5 O A:ACT1441 4.8 77.1 0.8 O A:ASP136 4.8 42.8 0.5 CB A:ASP136 4.8 43.6 0.5 CA A:ASP136 4.9 42.0 0.5 O A:TYR90 5.0 41.1 1.0

Sodium binding site 2 out of 2 in the Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate


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 Glycoprotein E1 in Its Post-Fusion Form Crystallized in Presence of 1MM of Calcium Acetate within 5.0Å range: probe atom residue distance (Å) B Occ C:Na1439 b:34.9 occ:0.57 CA C:CA1440 0.6 48.8 0.4 O C:HOH2084 2.0 51.1 1.0 O C:ALA89 2.2 41.3 1.0 OD2 C:ASP136 2.3 62.9 0.4 OD1 C:ASN88 2.3 43.3 1.0 OD1 C:ASP136 2.3 55.3 0.6 O C:THR137 2.6 42.0 0.6 O C:THR137 2.6 41.7 0.4 CG C:ASN88 3.3 49.9 1.0 CG C:ASP136 3.3 57.5 0.4 CG C:ASP136 3.5 55.7 0.6 C C:ALA89 3.5 42.2 1.0 C C:THR137 3.7 42.5 0.6 CB C:ASP136 3.8 47.1 0.4 C C:THR137 3.8 41.8 0.4 OD2 C:ASP136 4.0 60.1 0.6 ND2 C:ASN88 4.0 39.0 1.0 N C:SER91 4.1 45.3 1.0 N C:ALA89 4.1 35.9 1.0 C C:ASN88 4.2 38.5 1.0 N C:THR137 4.2 42.5 0.6 CG1 C:VAL138 4.3 41.0 0.6 CB C:ASN88 4.3 34.1 1.0 C C:TYR90 4.3 47.5 1.0 CG2 C:VAL138 4.4 40.3 0.4 N C:TYR90 4.4 40.5 1.0 CA C:ALA89 4.4 36.8 1.0 N C:THR137 4.4 41.0 0.4 O C:ASN88 4.4 37.8 1.0 OD1 C:ASP136 4.4 58.7 0.4 CA C:TYR90 4.5 41.8 1.0 C C:ASP136 4.5 46.4 0.4 CA C:THR137 4.5 41.0 0.6 O C:HOH2025 4.6 54.1 1.0 CB C:SER91 4.6 49.8 1.0 O C:HOH2083 4.6 46.3 1.0 C C:ASP136 4.6 47.9 0.6 N C:VAL138 4.6 37.3 0.6 N C:VAL138 4.6 36.8 0.4 CA C:VAL138 4.7 35.7 0.4 CA C:ASN88 4.7 34.7 1.0 CB C:ASP136 4.7 49.1 0.6 CA C:SER91 4.7 46.3 1.0 CA C:VAL138 4.7 36.2 0.6 CA C:THR137 4.8 39.5 0.4 O C:ASP136 4.8 46.0 0.4 CA C:ASP136 4.8 45.0 0.4 CA C:ASP136 4.8 47.1 0.6 O C:TYR90 5.0 47.1 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