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Calcium 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:

Sodium (Na) 1 atom

Calcium Binding Sites:

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 20MM of Calcium Acetate (pdb code 4b3v). 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 20MM of Calcium Acetate, PDB code: 4b3v:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4b3v

Go back to Calcium Binding Sites List in 4b3v
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 20MM 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 20MM of Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1451

b:33.4
occ:0.50
NA A:NA1450 0.1 41.5 0.5
OD2 A:ASP136 2.1 44.7 0.5
O A:THR137 2.3 29.5 0.5
O A:THR137 2.3 30.5 0.6
OD1 A:ASP136 2.3 41.7 0.6
O A:ALA89 2.3 28.6 1.0
OD1 A:ASN88 2.4 31.6 1.0
O A:HOH2118 2.6 40.6 1.0
CG A:ASP136 3.2 44.5 0.5
CG A:ASN88 3.4 39.4 1.0
C A:THR137 3.4 30.9 0.6
C A:THR137 3.5 29.9 0.5
CG A:ASP136 3.5 41.5 0.6
C A:ALA89 3.6 29.4 1.0
CB A:ASP136 3.6 33.6 0.5
N A:THR137 3.8 30.3 0.6
ND2 A:ASN88 4.0 29.4 1.0
C A:ASP136 4.1 35.1 0.6
CG1 A:VAL138 4.1 28.8 0.6
N A:THR137 4.1 28.3 0.5
C A:ASP136 4.2 33.2 0.5
N A:SER91 4.2 30.6 1.0
CA A:THR137 4.2 29.2 0.6
CG2 A:VAL138 4.2 28.6 0.5
C A:ASN88 4.2 27.5 1.0
N A:ALA89 4.3 24.6 1.0
OD1 A:ASP136 4.3 51.6 0.5
OD2 A:ASP136 4.3 47.0 0.6
CA A:ASP136 4.3 32.9 0.6
CB A:ASN88 4.3 23.8 1.0
N A:VAL138 4.3 25.4 0.5
N A:VAL138 4.4 25.9 0.6
CA A:THR137 4.4 27.2 0.5
C A:TYR90 4.4 32.7 1.0
N A:TYR90 4.4 27.0 1.0
O A:ASN88 4.4 26.9 1.0
CB A:ASP136 4.4 34.6 0.6
CA A:VAL138 4.5 24.5 0.5
CA A:TYR90 4.5 27.4 1.0
O A:ASP136 4.5 32.5 0.5
CA A:VAL138 4.5 24.9 0.6
CA A:ASP136 4.5 31.6 0.5
CA A:ALA89 4.5 24.6 1.0
O A:ASP136 4.6 34.8 0.6
CB A:SER91 4.7 34.8 1.0
O A:HOH2048 4.7 53.4 1.0
OXT A:ACT1443 4.8 48.2 0.6
CA A:ASN88 4.8 23.6 1.0
CA A:SER91 4.8 31.0 1.0
O A:HOH2117 4.8 32.3 1.0
O A:HOH2119 4.9 55.3 1.0
CB A:THR137 4.9 37.3 0.6
CB A:VAL138 5.0 28.8 0.6
CB A:VAL138 5.0 28.5 0.5

Calcium binding site 2 out of 3 in 4b3v

Go back to Calcium Binding Sites List in 4b3v
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 20MM 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 20MM of Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1445

b:36.4
occ:1.00
OD1 B:ASP136 2.1 56.8 1.0
O B:HOH2093 2.2 30.9 1.0
O B:ALA89 2.3 27.3 1.0
OD1 B:ASN88 2.3 28.9 1.0
O B:THR137 2.4 32.8 1.0
OXT B:ACT1443 2.8 65.2 1.0
CG B:ASP136 3.3 51.8 1.0
CG B:ASN88 3.3 39.0 1.0
C B:ALA89 3.5 27.9 1.0
C B:THR137 3.6 34.2 1.0
OD2 B:ASP136 3.8 52.1 1.0
C B:ACT1443 3.9 65.5 1.0
ND2 B:ASN88 3.9 28.7 1.0
N B:THR137 4.1 36.2 1.0
N B:SER91 4.1 26.8 1.0
CG1 B:VAL138 4.2 32.7 1.0
N B:ALA89 4.2 23.9 1.0
C B:ASN88 4.2 26.7 1.0
CB B:ASN88 4.3 23.2 1.0
C B:TYR90 4.4 29.1 1.0
N B:TYR90 4.4 24.5 1.0
CA B:THR137 4.4 34.5 1.0
CA B:TYR90 4.4 24.5 1.0
O B:ASN88 4.4 25.7 1.0
CB B:ASP136 4.5 43.6 1.0
C B:ASP136 4.5 42.4 1.0
CA B:ALA89 4.5 24.1 1.0
N B:VAL138 4.5 28.9 1.0
O B:HOH2092 4.6 33.1 1.0
CB B:SER91 4.6 30.6 1.0
O B:ACT1443 4.6 65.5 1.0
CA B:VAL138 4.6 27.7 1.0
O B:HOH2027 4.7 48.5 1.0
CA B:ASN88 4.7 23.1 1.0
CA B:SER91 4.7 27.2 1.0
CA B:ASP136 4.8 42.0 1.0
CH3 B:ACT1443 4.8 65.2 1.0

Calcium binding site 3 out of 3 in 4b3v

Go back to Calcium Binding Sites List in 4b3v
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 20MM 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 20MM of Calcium Acetate within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1446

b:36.4
occ:1.00
OD1 C:ASP136 2.1 51.8 1.0
O C:HOH2093 2.2 37.4 1.0
O C:ALA89 2.3 25.9 1.0
OD1 C:ASN88 2.3 27.7 1.0
O C:THR137 2.4 33.1 1.0
O C:ACT1444 2.9 71.3 1.0
CG C:ASP136 3.2 51.8 1.0
CG C:ASN88 3.3 37.8 1.0
C C:ALA89 3.5 26.8 1.0
C C:THR137 3.6 34.1 1.0
OD2 C:ASP136 3.8 57.1 1.0
ND2 C:ASN88 3.9 28.4 1.0
N C:THR137 4.1 35.1 1.0
C C:ACT1444 4.1 71.7 1.0
N C:SER91 4.1 27.9 1.0
CG1 C:VAL138 4.1 32.0 1.0
N C:ALA89 4.2 22.6 1.0
C C:ASN88 4.2 25.3 1.0
CB C:ASN88 4.3 20.6 1.0
C C:TYR90 4.4 30.0 1.0
CA C:THR137 4.4 33.7 1.0
CB C:ASP136 4.4 42.9 1.0
N C:TYR90 4.4 24.2 1.0
C C:ASP136 4.4 41.3 1.0
O C:ASN88 4.4 25.2 1.0
CA C:TYR90 4.5 24.4 1.0
CA C:ALA89 4.5 22.6 1.0
N C:VAL138 4.5 28.8 1.0
CA C:VAL138 4.6 27.5 1.0
CB C:SER91 4.6 32.1 1.0
O C:HOH2030 4.6 40.7 1.0
O C:HOH2092 4.7 34.6 1.0
CA C:ASP136 4.7 41.1 1.0
CA C:ASN88 4.7 21.2 1.0
OXT C:ACT1444 4.8 71.6 1.0
CA C:SER91 4.8 28.4 1.0
O C:ASP136 5.0 40.7 1.0

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: Sat Dec 12 04:40:29 2020

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