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Calcium in PDB 4ild: Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein

Protein crystallography data

The structure of Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein, PDB code: 4ild was solved by Y.Modis, Y.Li, J.Wang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 47.97 / 3.27
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 136.720, 54.450, 95.920, 90.00, 92.23, 90.00
R / Rfree (%) 24.6 / 28.9

Other elements in 4ild:

The structure of Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein also contains other interesting chemical elements:

Uranium (U) 4 atoms

Calcium Binding Sites:

The binding sites of Calcium atom in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein (pdb code 4ild). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein, PDB code: 4ild:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in 4ild

Go back to Calcium Binding Sites List in 4ild
Calcium binding site 1 out of 4 in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein


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 Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2409

b:41.7
occ:1.00
OD2 A:ASP788 2.7 63.9 1.0
CB A:ASP788 3.5 57.3 1.0
CG A:ASP788 3.5 63.0 1.0
OD1 A:ASN790 3.8 52.1 1.0
CA A:PHE791 4.4 39.7 1.0
N A:PHE791 4.7 41.5 1.0
O A:ASN790 4.7 42.1 1.0
OD1 A:ASP788 4.7 67.7 1.0
C A:ASN790 4.8 42.9 1.0
CA A:ASP788 4.9 54.5 1.0

Calcium binding site 2 out of 4 in 4ild

Go back to Calcium Binding Sites List in 4ild
Calcium binding site 2 out of 4 in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein


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 Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2410

b:14.5
occ:1.00
OD1 A:ASP885 2.6 43.9 1.0
OD2 A:ASP885 2.8 45.7 1.0
CG A:ASP885 3.0 42.4 1.0
CB A:ASP885 4.5 38.4 1.0
O A:GLN886 4.5 35.0 1.0
N A:GLN886 4.9 32.3 1.0

Calcium binding site 3 out of 4 in 4ild

Go back to Calcium Binding Sites List in 4ild
Calcium binding site 3 out of 4 in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein


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 Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Ca2411

b:30.6
occ:1.00
CA A:LEU947 3.6 30.9 1.0
CB A:LEU947 3.7 29.3 1.0
CE A:LYS948 3.7 46.1 1.0
O A:THR946 4.0 37.3 1.0
N A:LYS948 4.0 30.3 1.0
CG A:LYS948 4.1 39.4 1.0
C A:LEU947 4.4 29.9 1.0
CD A:LYS948 4.5 42.9 1.0
N A:LEU947 4.7 31.5 1.0
C A:THR946 4.7 34.9 1.0
NZ A:LYS948 4.9 48.3 1.0
CE A:LYS993 5.0 44.0 1.0

Calcium binding site 4 out of 4 in 4ild

Go back to Calcium Binding Sites List in 4ild
Calcium binding site 4 out of 4 in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Ca2409

b:30.7
occ:1.00
OD2 B:ASP1021 2.5 70.6 1.0
OD1 B:ASP1021 2.7 74.2 1.0
CG B:ASP1021 3.0 71.0 1.0
CB B:ASP1021 4.5 66.1 1.0
N B:LEU1022 4.9 76.2 1.0

Reference:

Y.Li, J.Wang, R.Kanai, Y.Modis. Crystal Structure of Glycoprotein E2 From Bovine Viral Diarrhea Virus. Proc.Natl.Acad.Sci.Usa V. 110 6805 2013.
ISSN: ISSN 0027-8424
PubMed: 23569276
DOI: 10.1073/PNAS.1300524110
Page generated: Wed Oct 28 08:43:55 2020

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