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Calcium in PDB 4adg: Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II)

Protein crystallography data

The structure of Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II), PDB code: 4adg 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 / 2.18
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 121.680, 126.550, 130.020, 90.00, 90.00, 90.00
R / Rfree (%) 17.79 / 19.34

Other elements in 4adg:

The structure of Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II) (pdb code 4adg). 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 Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II), PDB code: 4adg:
Jump to Calcium binding site number: 1; 2; 3;

Calcium binding site 1 out of 3 in 4adg

Go back to Calcium Binding Sites List in 4adg
Calcium binding site 1 out of 3 in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II)


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 Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca1437

b:30.5
occ:1.00
O A:HOH2118 2.2 30.6 1.0
OD1 A:ASP136 2.3 41.5 1.0
O A:THR137 2.3 28.4 1.0
O A:ALA89 2.3 28.8 1.0
OD1 A:ASN88 2.3 25.5 1.0
OXT A:ACT1438 2.6 43.2 1.0
CG A:ASN88 3.3 35.3 1.0
CG A:ASP136 3.5 41.7 1.0
C A:THR137 3.5 29.4 1.0
C A:ALA89 3.6 29.3 1.0
C A:ACT1438 3.7 43.6 1.0
N A:THR137 3.9 29.5 1.0
ND2 A:ASN88 4.0 25.7 1.0
OD2 A:ASP136 4.1 47.1 1.0
N A:SER91 4.1 28.9 1.0
CA A:THR137 4.2 28.2 1.0
C A:ASP136 4.3 34.5 1.0
N A:ALA89 4.3 24.0 1.0
CG1 A:VAL138 4.3 27.6 1.0
C A:ASN88 4.3 26.5 1.0
C A:TYR90 4.4 31.8 1.0
CB A:ASN88 4.4 21.2 1.0
N A:TYR90 4.4 26.8 1.0
N A:VAL138 4.4 24.7 1.0
CA A:TYR90 4.5 27.2 1.0
O A:ACT1438 4.5 44.5 1.0
O A:ASN88 4.5 25.9 1.0
CB A:ASP136 4.6 35.0 1.0
CA A:ALA89 4.6 24.5 1.0
CB A:SER91 4.6 33.1 1.0
CA A:ASP136 4.6 33.2 1.0
CA A:VAL138 4.7 23.5 1.0
CH3 A:ACT1438 4.7 43.4 1.0
CA A:SER91 4.8 29.2 1.0
O A:HOH2041 4.8 46.3 1.0
CB A:THR137 4.8 35.6 1.0
O A:ASP136 4.8 34.0 1.0
CA A:ASN88 4.8 22.0 1.0
O A:HOH2119 4.9 30.6 1.0

Calcium binding site 2 out of 3 in 4adg

Go back to Calcium Binding Sites List in 4adg
Calcium binding site 2 out of 3 in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II)


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 Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca1439

b:27.9
occ:1.00
O B:HOH2097 2.2 29.9 1.0
OD1 B:ASP136 2.2 40.5 1.0
O B:ALA89 2.3 26.5 1.0
OD1 B:ASN88 2.3 27.3 1.0
O B:THR137 2.3 26.9 1.0
OXT B:ACT1440 2.5 41.5 1.0
CG B:ASN88 3.4 33.5 1.0
CG B:ASP136 3.4 36.7 1.0
C B:ALA89 3.5 26.6 1.0
C B:THR137 3.5 27.7 1.0
C B:ACT1440 3.7 42.4 1.0
OD2 B:ASP136 4.0 35.9 1.0
ND2 B:ASN88 4.0 22.7 1.0
N B:THR137 4.0 27.7 1.0
N B:SER91 4.1 24.8 1.0
N B:ALA89 4.2 21.7 1.0
C B:ASN88 4.3 24.4 1.0
CG1 B:VAL138 4.3 26.1 1.0
CA B:THR137 4.3 26.4 1.0
C B:TYR90 4.3 27.1 1.0
C B:ASP136 4.3 33.0 1.0
N B:TYR90 4.4 23.1 1.0
CA B:TYR90 4.4 23.0 1.0
CB B:ASN88 4.4 19.8 1.0
CA B:ALA89 4.5 21.9 1.0
O B:ASN88 4.5 23.8 1.0
N B:VAL138 4.5 23.1 1.0
O B:ACT1440 4.5 43.1 1.0
CH3 B:ACT1440 4.5 42.5 1.0
CB B:ASP136 4.5 32.8 1.0
CB B:SER91 4.5 29.0 1.0
O B:HOH2023 4.6 47.3 1.0
CA B:ASP136 4.6 31.7 1.0
CA B:VAL138 4.7 22.0 1.0
CA B:SER91 4.7 25.1 1.0
CA B:ASN88 4.8 20.2 1.0
O B:HOH2098 4.8 25.2 1.0
O B:ASP136 4.9 32.3 1.0
CB B:THR137 4.9 34.1 1.0

Calcium binding site 3 out of 3 in 4adg

Go back to Calcium Binding Sites List in 4adg
Calcium binding site 3 out of 3 in the Crystal Structure of the Rubella Virus Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II)


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 Envelope Glycoprotein E1 in Post-Fusion Form (Crystal Form II) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Ca1444

b:28.1
occ:1.00
O C:HOH2089 2.2 27.4 1.0
OD1 C:ASP136 2.2 41.5 1.0
O C:ALA89 2.3 27.5 1.0
OD1 C:ASN88 2.3 27.0 1.0
O C:THR137 2.4 28.3 1.0
O C:ACT1446 2.6 39.7 1.0
CG C:ASN88 3.3 34.7 1.0
CG C:ASP136 3.4 41.9 1.0
C C:ALA89 3.5 28.0 1.0
C C:THR137 3.6 28.9 1.0
C C:ACT1446 3.8 40.4 1.0
ND2 C:ASN88 4.0 24.2 1.0
N C:THR137 4.0 28.6 1.0
OD2 C:ASP136 4.0 47.2 1.0
N C:SER91 4.1 27.8 1.0
N C:ALA89 4.2 23.2 1.0
C C:ASN88 4.3 25.8 1.0
CG1 C:VAL138 4.3 26.8 1.0
CA C:THR137 4.3 27.3 1.0
C C:TYR90 4.4 30.2 1.0
N C:TYR90 4.4 25.3 1.0
C C:ASP136 4.4 33.7 1.0
CB C:ASN88 4.4 20.3 1.0
CA C:TYR90 4.4 25.6 1.0
O C:ASN88 4.5 25.4 1.0
CA C:ALA89 4.5 23.6 1.0
OXT C:ACT1446 4.5 41.4 1.0
N C:VAL138 4.5 23.8 1.0
CB C:ASP136 4.5 34.6 1.0
CB C:SER91 4.6 32.3 1.0
CA C:ASP136 4.7 32.9 1.0
O C:HOH2090 4.7 28.5 1.0
O C:HOH2028 4.7 44.3 1.0
CA C:SER91 4.7 28.4 1.0
CA C:VAL138 4.7 22.5 1.0
CH3 C:ACT1446 4.7 39.9 1.0
CA C:ASN88 4.8 21.2 1.0
CB C:THR137 4.9 34.1 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 04:38:46 2020

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