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Sodium in PDB 4b3v: Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post- Fusion Form Crystallized in Presence of 20MM of Calcium Acetate

Protein crystallography data

The structure of Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post- Fusion Form Crystallized in Presence of 20MM of Calcium Acetate, PDB code: 4b3v was solved by M.C.Vaney, R.M.Dubois, M.A.Tortorici, F.A.Rey, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 28.99 / 1.98
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.272, 126.163, 129.375, 90.00, 90.00, 90.00
R / Rfree (%) 18.5 / 19.8

Other elements in 4b3v:

The structure of Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post- Fusion Form Crystallized in Presence of 20MM of Calcium Acetate also contains other interesting chemical elements:

Calcium (Ca) 3 atoms

Sodium Binding Sites:

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 20MM of Calcium Acetate (pdb code 4b3v). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total only one binding site of Sodium was determined in the Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post- Fusion Form Crystallized in Presence of 20MM of Calcium Acetate, PDB code: 4b3v:

Sodium binding site 1 out of 1 in 4b3v

Go back to Sodium Binding Sites List in 4b3v
Sodium binding site 1 out of 1 in the Crystal Structure of the Rubella Virus Glycoprotein E1 in Its Post- Fusion Form Crystallized in Presence of 20MM 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 20MM of Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na1450

b:41.5
occ:0.50
CA A:CA1451 0.1 33.4 0.5
OD2 A:ASP136 2.2 44.7 0.5
O A:ALA89 2.3 28.6 1.0
OD1 A:ASN88 2.3 31.6 1.0
O A:THR137 2.3 29.5 0.5
O A:THR137 2.4 30.5 0.6
OD1 A:ASP136 2.4 41.7 0.6
O A:HOH2118 2.5 40.6 1.0
CG A:ASN88 3.3 39.4 1.0
CG A:ASP136 3.3 44.5 0.5
C A:ALA89 3.5 29.4 1.0
C A:THR137 3.5 30.9 0.6
C A:THR137 3.5 29.9 0.5
CG A:ASP136 3.6 41.5 0.6
CB A:ASP136 3.7 33.6 0.5
ND2 A:ASN88 3.9 29.4 1.0
N A:THR137 3.9 30.3 0.6
CG1 A:VAL138 4.1 28.8 0.6
C A:ASN88 4.1 27.5 1.0
N A:ALA89 4.1 24.6 1.0
N A:THR137 4.2 28.3 0.5
N A:SER91 4.2 30.6 1.0
C A:ASP136 4.2 35.1 0.6
CB A:ASN88 4.3 23.8 1.0
C A:ASP136 4.3 33.2 0.5
CA A:THR137 4.3 29.2 0.6
CG2 A:VAL138 4.3 28.6 0.5
O A:ASN88 4.4 26.9 1.0
N A:TYR90 4.4 27.0 1.0
OD1 A:ASP136 4.4 51.6 0.5
OD2 A:ASP136 4.4 47.0 0.6
N A:VAL138 4.4 25.4 0.5
C A:TYR90 4.4 32.7 1.0
N A:VAL138 4.4 25.9 0.6
CA A:ALA89 4.4 24.6 1.0
CA A:ASP136 4.4 32.9 0.6
CA A:TYR90 4.5 27.4 1.0
CA A:VAL138 4.5 24.5 0.5
CA A:THR137 4.5 27.2 0.5
CA A:VAL138 4.6 24.9 0.6
CB A:ASP136 4.6 34.6 0.6
O A:HOH2048 4.6 53.4 1.0
CA A:ASP136 4.6 31.6 0.5
O A:ASP136 4.7 32.5 0.5
CA A:ASN88 4.7 23.6 1.0
O A:HOH2117 4.7 32.3 1.0
CB A:SER91 4.7 34.8 1.0
O A:ASP136 4.8 34.8 0.6
CA A:SER91 4.8 31.0 1.0
OXT A:ACT1443 4.9 48.2 0.6
O A:HOH2119 4.9 55.3 1.0
CB A:THR137 5.0 37.3 0.6
CB A:VAL138 5.0 28.8 0.6

Reference:

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
Page generated: Tue Dec 15 06:33:36 2020

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