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Uranium in PDB 3pto: Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex

Protein crystallography data

The structure of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex, PDB code: 3pto was solved by M.Luo, T.J.Green, M.Rowse, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 38.76 / 3.01
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 165.643, 234.062, 75.975, 90.00, 90.00, 90.00
R / Rfree (%) 25.8 / 29.1

Uranium Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 15;

Binding sites:

The binding sites of Uranium atom in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex (pdb code 3pto). This binding sites where shown within 5.0 Angstroms radius around Uranium atom.
In total 15 binding sites of Uranium where determined in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex, PDB code: 3pto:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Uranium binding site 1 out of 15 in 3pto

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Uranium binding site 1 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


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 An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U1

b:0.0
occ:1.00
OE1 A:GLN57 4.3 0.3 1.0
CD A:GLN57 4.7 0.7 1.0
NE2 A:GLN57 4.9 0.8 1.0

Uranium binding site 2 out of 15 in 3pto

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Uranium binding site 2 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


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Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 2 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U423

b:0.5
occ:1.00
CB B:ASP123 4.0 0.4 1.0
CA B:ASP123 4.2 0.7 1.0
OE1 B:GLN57 4.3 0.3 1.0
OG B:SER125 4.5 0.1 1.0
C B:ASP123 4.5 0.4 1.0
CG B:ASP123 4.7 0.2 1.0
O B:ASP123 4.7 1.0 1.0
OD2 B:ASP123 4.9 0.8 1.0
CD B:GLN57 5.0 0.1 1.0
CB B:SER125 5.0 1.0 1.0

Uranium binding site 3 out of 15 in 3pto

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Uranium binding site 3 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


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 An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:U423

b:0.2
occ:1.00
NE2 C:GLN57 4.4 0.1 1.0
OE1 C:GLN57 4.5 0.7 1.0
CD C:GLN57 4.5 0.7 1.0

Uranium binding site 4 out of 15 in 3pto

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Uranium binding site 4 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


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 An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:U423

b:0.6
occ:1.00
CA D:ASP123 3.4 0.6 1.0
CB D:ASP123 3.5 0.2 1.0
C D:ASP123 3.8 0.9 1.0
O D:ASP123 4.2 0.6 1.0
CG D:ASP123 4.2 0.9 1.0
N D:ALA124 4.4 0.5 1.0
OG D:SER125 4.4 0.7 1.0
OE1 D:GLN57 4.4 0.3 1.0
OD2 D:ASP123 4.6 1.0 1.0
N D:ASP123 4.7 0.9 1.0
OD1 D:ASP123 4.9 0.1 1.0
CB D:SER125 4.9 0.6 1.0

Uranium binding site 5 out of 15 in 3pto

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Uranium binding site 5 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 5 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
E:U423

b:0.1
occ:1.00
OE1 E:GLN57 4.1 0.7 1.0
CD E:GLN57 4.4 0.9 1.0
NE2 E:GLN57 4.5 0.5 1.0

Uranium binding site 6 out of 15 in 3pto

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Uranium binding site 6 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 6 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
C:U424

b:0.1
occ:1.00
OE1 B:GLU323 2.5 91.6 1.0
OD1 C:ASP343 2.7 86.0 1.0
OE2 B:GLU253 2.9 85.1 1.0
CG C:ASP343 3.1 94.7 1.0
OD2 C:ASP343 3.4 92.8 1.0
CD B:GLU323 3.6 90.9 1.0
CD B:GLU253 3.8 97.0 1.0
OE1 B:GLU253 4.0 0.8 1.0
OE2 B:GLU323 4.1 87.0 1.0
CB C:ASP343 4.1 88.3 1.0
N B:ARG252 4.6 76.7 1.0
CB B:ASN251 4.6 68.6 1.0
CB B:ARG252 4.6 83.8 1.0
CG B:GLU323 4.8 78.9 1.0
CA C:GLY239 4.8 73.7 1.0
CB B:GLU323 4.8 70.0 1.0
N B:GLU253 5.0 75.5 1.0

Uranium binding site 7 out of 15 in 3pto

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Uranium binding site 7 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 7 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U424

b:0.4
occ:1.00
OE1 A:GLU323 2.6 91.8 1.0
OD1 B:ASP343 2.9 85.0 1.0
OE2 A:GLU253 3.0 86.0 1.0
CG B:ASP343 3.2 94.3 1.0
OD2 B:ASP343 3.4 93.7 1.0
CD A:GLU323 3.7 89.7 1.0
CD A:GLU253 3.9 97.9 1.0
OE2 A:GLU323 4.1 85.2 1.0
OE1 A:GLU253 4.1 1.0 1.0
CB B:ASP343 4.1 88.1 1.0
CB A:ARG252 4.6 83.8 1.0
N A:ARG252 4.6 74.3 1.0
CB A:ASN251 4.6 67.8 1.0
CA B:GLY239 4.9 73.1 1.0
CG A:GLU323 5.0 78.0 1.0

Uranium binding site 8 out of 15 in 3pto

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Uranium binding site 8 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 8 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:U424

b:0.6
occ:1.00
OE1 C:GLU323 2.6 91.0 1.0
OD1 D:ASP343 2.8 88.8 1.0
OE2 C:GLU253 3.0 87.6 1.0
CG D:ASP343 3.1 95.9 1.0
OD2 D:ASP343 3.2 96.1 1.0
CD C:GLU323 3.7 90.3 1.0
CD C:GLU253 3.9 95.5 1.0
OE1 C:GLU253 4.1 0.1 1.0
CB D:ASP343 4.1 86.0 1.0
OE2 C:GLU323 4.2 84.9 1.0
CB C:ARG252 4.6 84.1 1.0
N C:ARG252 4.6 76.0 1.0
CB C:ASN251 4.7 68.2 1.0
CA D:GLY239 4.8 72.5 1.0
CG C:GLU323 4.9 78.9 1.0
O D:GLY239 5.0 71.7 1.0
CB C:GLU323 5.0 68.1 1.0

Uranium binding site 9 out of 15 in 3pto

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Uranium binding site 9 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 9 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
D:U425

b:0.5
occ:1.00
OE1 D:GLU323 2.7 91.9 1.0
OE2 D:GLU253 2.8 86.5 1.0
CD D:GLU253 3.7 95.4 1.0
CD D:GLU323 3.8 90.3 1.0
OE1 D:GLU253 3.8 0.5 1.0
OE2 D:GLU323 4.3 82.3 1.0
CB D:ARG252 4.5 83.9 1.0
N D:ARG252 4.6 76.7 1.0
CB D:ASN251 4.7 68.0 1.0
N D:GLU253 4.9 75.3 1.0
CG D:GLU323 5.0 79.4 1.0

Uranium binding site 10 out of 15 in 3pto

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Uranium binding site 10 out of 15 in the Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 10 of Crystal Structure of An Empty Vesicular Stomatitis Virus Nucleocapsid Protein Complex within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U423

b:0.6
occ:1.00
OE1 E:GLU323 2.7 92.0 1.0
OE2 E:GLU253 2.9 84.2 1.0
OD1 A:ASP343 2.9 88.3 1.0
CG A:ASP343 3.2 94.6 1.0
OD2 A:ASP343 3.3 92.2 1.0
CD E:GLU253 3.7 94.7 1.0
CD E:GLU323 3.8 91.0 1.0
OE1 E:GLU253 3.9 0.0 1.0
CB A:ASP343 4.1 86.1 1.0
OE2 E:GLU323 4.3 86.2 1.0
CB E:ARG252 4.4 83.7 1.0
N E:ARG252 4.5 74.2 1.0
CB E:ASN251 4.7 69.0 1.0
CA A:GLY239 4.8 73.8 1.0
N E:GLU253 4.9 77.7 1.0

Reference:

T.J.Green, M.Rowse, J.Tsao, J.Kang, P.Ge, Z.H.Zhou, M.Luo. Access to Rna Encapsidated in the Nucleocapsid of Vesicular Stomatitis Virus. J.Virol. V. 85 2714 2011.
ISSN: ISSN 0022-538X
PubMed: 21177817
DOI: 10.1128/JVI.01927-10
Page generated: Thu Oct 29 07:03:50 2020

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