Calcium 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:

Sodium

(Na)

2 atoms

The binding sites of Calcium 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 Calcium atom.
In total 3 binding sites of Calcium 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 Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 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 Calcium with other atoms in the Ca 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:Ca1440 b:55.7 occ:0.55 NA A:NA1439 0.5 26.9 0.5 OD2 A:ASP136 2.0 56.0 0.5 O A:THR137 2.2 39.1 0.5 OD1 A:ASP136 2.2 50.7 0.5 O A:THR137 2.3 39.6 0.5 O A:ALA89 2.4 37.1 1.0 O A:HOH2114 2.5 45.8 1.0 OD1 A:ASN88 2.6 40.9 1.0 CG A:ASP136 3.0 55.7 0.5 C A:THR137 3.3 39.7 0.5 CG A:ASP136 3.3 50.9 0.5 C A:THR137 3.4 39.9 0.5 CG A:ASN88 3.5 50.2 1.0 CB A:ASP136 3.5 44.3 0.5 C A:ALA89 3.6 38.0 1.0 N A:THR137 3.8 38.9 0.5 OD2 A:ASP136 3.9 56.4 0.5 CG1 A:VAL138 3.9 38.2 0.5 CG2 A:VAL138 4.0 38.7 0.5 C A:ASP136 4.1 43.6 0.5 N A:THR137 4.1 38.6 0.5 CA A:THR137 4.1 37.9 0.5 ND2 A:ASN88 4.1 41.2 1.0 C A:ASP136 4.1 43.6 0.5 N A:SER91 4.1 38.8 1.0 OD1 A:ASP136 4.2 63.0 0.5 N A:VAL138 4.2 35.0 0.5 N A:VAL138 4.3 35.4 0.5 CA A:VAL138 4.3 34.5 0.5 O A:ASP136 4.3 42.8 0.5 C A:ASN88 4.3 36.2 1.0 CA A:VAL138 4.4 34.1 0.5 CB A:ASP136 4.4 43.6 0.5 N A:ALA89 4.4 33.7 1.0 CA A:THR137 4.4 37.4 0.5 CB A:ASN88 4.4 33.0 1.0 O A:ACT1441 4.4 77.1 0.8 CA A:TYR90 4.4 35.8 1.0 CA A:ASP136 4.4 42.2 0.5 C A:TYR90 4.4 41.3 1.0 O A:ASN88 4.5 35.6 1.0 N A:TYR90 4.5 35.4 1.0 CA A:ASP136 4.5 42.0 0.5 CB A:SER91 4.6 43.0 1.0 CA A:ALA89 4.6 33.9 1.0 O A:ASP136 4.7 42.8 0.5 CB A:VAL138 4.8 38.5 0.5 CB A:THR137 4.8 47.4 0.5 O A:HOH2042 4.8 62.2 1.0 CB A:VAL138 4.8 38.1 0.5 CA A:SER91 4.8 39.7 1.0 CA A:ASN88 4.9 32.2 1.0

Calcium binding site 2 out of 3 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 Calcium with other atoms in the Ca 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 B:Ca1438 b:43.7 occ:1.00 O B:HOH2094 2.2 51.3 1.0 OD1 B:ASP136 2.3 58.0 1.0 O B:ALA89 2.3 36.1 1.0 O B:THR137 2.3 42.5 1.0 OD1 B:ASN88 2.4 42.6 1.0 OXT B:ACT1439 2.8 84.8 1.0 CG B:ASN88 3.3 49.5 1.0 CG B:ASP136 3.4 58.8 1.0 C B:THR137 3.5 43.7 1.0 C B:ALA89 3.5 37.0 1.0 C B:ACT1439 3.9 84.9 1.0 ND2 B:ASN88 4.0 40.4 1.0 OD2 B:ASP136 4.0 62.1 1.0 N B:THR137 4.0 45.7 1.0 N B:SER91 4.1 36.4 1.0 CG1 B:VAL138 4.1 41.0 1.0 C B:ASN88 4.2 35.8 1.0 N B:ALA89 4.2 33.0 1.0 CA B:THR137 4.3 44.2 1.0 CB B:ASN88 4.3 32.4 1.0 C B:TYR90 4.4 38.4 1.0 N B:TYR90 4.4 33.9 1.0 N B:VAL138 4.4 37.9 1.0 O B:ASN88 4.4 35.5 1.0 CA B:TYR90 4.4 34.2 1.0 C B:ASP136 4.4 52.1 1.0 CA B:ALA89 4.5 33.2 1.0 CA B:VAL138 4.6 36.3 1.0 CB B:SER91 4.6 40.4 1.0 CB B:ASP136 4.6 53.5 1.0 O B:HOH2026 4.6 59.0 1.0 O B:ACT1439 4.7 85.9 1.0 CA B:ASN88 4.7 31.0 1.0 CH3 B:ACT1439 4.7 84.7 1.0 CA B:ASP136 4.7 52.0 1.0 O B:HOH2093 4.8 38.7 1.0 CA B:SER91 4.8 36.9 1.0 CB B:THR137 4.9 53.6 1.0 O B:ASP136 5.0 51.9 1.0 CB B:VAL138 5.0 40.7 1.0

Calcium binding site 3 out of 3 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 Calcium with other atoms in the Ca binding site number 3 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:Ca1440 b:48.8 occ:0.43 NA C:NA1439 0.6 34.9 0.6 O C:THR137 2.2 42.0 0.6 OD2 C:ASP136 2.2 62.9 0.4 OD1 C:ASP136 2.2 55.3 0.6 O C:ALA89 2.2 41.3 1.0 O C:THR137 2.3 41.7 0.4 O C:HOH2084 2.6 51.1 1.0 OD1 C:ASN88 2.6 43.3 1.0 CG C:ASP136 3.2 55.7 0.6 C C:THR137 3.3 42.5 0.6 CG C:ASP136 3.3 57.5 0.4 C C:THR137 3.4 41.8 0.4 C C:ALA89 3.4 42.2 1.0 CG C:ASN88 3.5 49.9 1.0 OD2 C:ASP136 3.7 60.1 0.6 CG1 C:VAL138 3.8 41.0 0.6 CG2 C:VAL138 3.8 40.3 0.4 CB C:ASP136 3.8 47.1 0.4 N C:THR137 3.8 42.5 0.6 N C:VAL138 4.1 37.3 0.6 C C:ASN88 4.1 38.5 1.0 ND2 C:ASN88 4.1 39.0 1.0 CA C:THR137 4.1 41.0 0.6 N C:VAL138 4.2 36.8 0.4 N C:SER91 4.2 45.3 1.0 CA C:VAL138 4.2 35.7 0.4 N C:ALA89 4.2 35.9 1.0 N C:THR137 4.2 41.0 0.4 C C:ASP136 4.2 47.9 0.6 CA C:VAL138 4.2 36.2 0.6 O C:ASN88 4.2 37.8 1.0 C C:ASP136 4.2 46.4 0.4 N C:TYR90 4.3 40.5 1.0 CB C:ASN88 4.3 34.1 1.0 CA C:TYR90 4.3 41.8 1.0 OD1 C:ASP136 4.4 58.7 0.4 C C:TYR90 4.4 47.5 1.0 CA C:ALA89 4.4 36.8 1.0 CB C:ASP136 4.4 49.1 0.6 O C:ASP136 4.4 46.0 0.4 CA C:THR137 4.5 39.5 0.4 CB C:VAL138 4.6 39.9 0.4 CA C:ASP136 4.6 47.1 0.6 CB C:VAL138 4.6 40.6 0.6 CA C:ASP136 4.7 45.0 0.4 CA C:ASN88 4.7 34.7 1.0 CB C:SER91 4.8 49.8 1.0 O C:ASP136 4.8 47.0 0.6 CB C:THR137 4.9 49.7 0.6 CA C:SER91 4.9 46.3 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