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Uranium 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:

Calcium (Ca) 4 atoms

Uranium Binding Sites:

The binding sites of Uranium 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 Uranium atom.
In total 4 binding sites of Uranium where determined in the Crystal Structure of Truncated Bovine Viral Diarrhea Virus 1 E2 Envelope Protein, PDB code: 4ild:
Jump to Uranium binding site number: 1; 2; 3; 4;

Uranium binding site 1 out of 4 in 4ild

Go back to Uranium Binding Sites List in 4ild
Uranium 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 Uranium with other atoms in the U 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
B:U2410

b:17.9
occ:0.50
U B:IUM2410 0.0 17.9 0.5
OE2 B:GLU974 1.7 54.0 1.0
O1 B:IUM2410 2.3 12.8 0.5
O2 B:IUM2410 2.3 15.4 0.5
CD B:GLU974 2.7 53.2 1.0
OE1 B:GLU974 3.1 55.7 1.0
CG B:GLU974 3.9 50.6 1.0

Uranium binding site 2 out of 4 in 4ild

Go back to Uranium Binding Sites List in 4ild
Uranium 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 Uranium with other atoms in the U 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
B:U2411

b:93.9
occ:0.50
U B:IUM2411 0.0 93.9 0.5
OE2 B:GLU908 1.7 73.5 1.0
O2 B:IUM2411 2.2 56.3 0.5
O1 B:IUM2411 2.2 68.5 0.5
CD B:GLU908 2.7 70.2 1.0
OE1 B:GLU906 2.9 0.6 1.0
CD B:LYS953 3.3 67.4 1.0
NZ B:LYS953 3.3 72.9 1.0
O1 B:IUM2412 3.3 72.5 0.5
OE1 B:GLU908 3.5 69.7 1.0
CG B:GLU908 3.7 64.3 1.0
CE B:LYS953 3.8 69.0 1.0
CD B:GLU906 4.1 98.8 1.0
CG B:LYS953 4.2 63.4 1.0
U B:IUM2412 4.4 80.8 0.5
CB B:LYS953 4.6 62.9 1.0
OE2 B:GLU906 4.7 98.0 1.0
CB B:GLU908 4.8 57.1 1.0
CB B:GLU906 4.8 82.7 1.0

Uranium binding site 3 out of 4 in 4ild

Go back to Uranium Binding Sites List in 4ild
Uranium 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 Uranium with other atoms in the U 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
B:U2412

b:80.8
occ:0.50
U B:IUM2412 0.0 80.8 0.5
O1 B:IUM2412 2.2 72.5 0.5
O2 B:IUM2412 2.2 60.2 0.5
CB B:GLU906 3.9 82.7 1.0
OE1 B:GLU906 4.3 0.6 1.0
N B:SER907 4.3 58.5 1.0
CD B:GLU906 4.3 98.8 1.0
CG B:GLU906 4.4 92.6 1.0
U B:IUM2411 4.4 93.9 0.5
O1 B:IUM2411 4.6 68.5 0.5
OE2 B:GLU908 4.6 73.5 1.0
CA B:GLU906 4.6 72.8 1.0
CG B:GLU908 4.7 64.3 1.0
OE2 B:GLU906 4.9 98.0 1.0
C B:GLU906 5.0 62.2 1.0

Uranium binding site 4 out of 4 in 4ild

Go back to Uranium Binding Sites List in 4ild
Uranium 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 Uranium with other atoms in the U 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:U2413

b:1.0
occ:0.50
U B:IUM2413 0.0 1.0 0.5
OD1 B:ASP799 2.1 64.6 1.0
O1 B:IUM2413 2.2 63.2 0.5
O2 B:IUM2413 2.3 65.1 0.5
CG B:ASP799 3.1 63.1 1.0
OD2 B:ASP799 3.6 58.8 1.0
NZ B:LYS801 4.1 49.0 1.0
CB B:ASP799 4.4 65.4 1.0
CA B:ASP799 4.8 62.5 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 Dec 16 02:29:58 2020

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