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Uranium in PDB 6bjy: Vsv Nucleocapsid with Polyamide Bound

Protein crystallography data

The structure of Vsv Nucleocapsid with Polyamide Bound, PDB code: 6bjy was solved by R.H.Gumpper, M.Luo, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 46.30 / 3.46
Space group P 2 21 21
Cell size a, b, c (Å), α, β, γ (°) 75.480, 165.480, 234.460, 90.00, 90.00, 90.00
R / Rfree (%) 26.6 / 31.1

Uranium Binding Sites:

Pages:

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

Binding sites:

The binding sites of Uranium atom in the Vsv Nucleocapsid with Polyamide Bound (pdb code 6bjy). This binding sites where shown within 5.0 Angstroms radius around Uranium atom.
In total 15 binding sites of Uranium where determined in the Vsv Nucleocapsid with Polyamide Bound, PDB code: 6bjy:
Jump to Uranium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Uranium binding site 1 out of 15 in 6bjy

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Uranium binding site 1 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 1 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U501

b:0.2
occ:1.00
OD1 A:ASP123 3.8 0.1 1.0
CG A:ASP123 3.8 0.9 1.0
OD2 A:ASP123 4.0 0.9 1.0
NE2 A:GLN57 4.4 74.8 1.0
OE1 A:GLN57 4.5 86.0 1.0
CB A:ASP123 4.5 0.8 1.0
CD A:GLN57 4.7 88.8 1.0

Uranium binding site 2 out of 15 in 6bjy

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Uranium binding site 2 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 2 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U502

b:0.2
occ:1.00
OD2 B:ASP343 2.9 75.0 1.0
OE2 A:GLU253 3.1 0.7 1.0
OE1 A:GLU323 3.4 79.7 1.0
OE1 A:GLU253 3.4 0.8 1.0
CD A:GLU253 3.6 0.3 1.0
CG B:ASP343 3.7 0.7 1.0
CB A:ARG252 4.0 0.2 1.0
O B:GLY239 4.4 87.3 1.0
CB B:ASP343 4.4 0.9 1.0
OD1 B:ASP343 4.5 88.6 1.0
CD A:GLU323 4.5 92.2 1.0
N A:ARG252 4.6 0.2 1.0
OE2 A:GLU323 4.9 95.7 1.0
CA A:ARG252 4.9 100.0 1.0

Uranium binding site 3 out of 15 in 6bjy

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Uranium binding site 3 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 3 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U503

b:0.1
occ:1.00
OD2 A:ASP358 3.2 0.1 1.0
O A:ASP358 3.4 0.7 1.0
OD1 E:ASP384 3.5 0.5 1.0
CG A:ASP358 3.8 0.4 1.0
OD1 A:ASP358 4.0 0.7 1.0
CG E:ASP384 4.5 0.6 1.0
C A:ASP358 4.5 0.4 1.0
O A:ASP359 4.7 0.2 1.0
OD2 E:ASP384 4.8 0.5 1.0
O E:GLY380 4.9 84.9 1.0
CB A:ASP358 4.9 0.7 1.0
CB A:ASP359 4.9 0.2 1.0
C A:ASP359 5.0 0.8 1.0

Uranium binding site 4 out of 15 in 6bjy

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Uranium binding site 4 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 4 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U504

b:0.9
occ:1.00
OD1 A:ASP384 3.1 0.6 1.0
CG B:ASP358 3.4 0.5 1.0
OD1 B:ASP358 3.4 0.8 1.0
OD2 B:ASP358 3.6 0.1 1.0
C B:ASP358 3.8 0.7 1.0
CB B:ASP358 3.9 0.1 1.0
CG A:ASP384 4.2 0.8 1.0
CA B:ASP358 4.5 0.8 1.0
O B:ASP358 4.5 0.9 1.0
OD2 A:ASP384 4.7 0.8 1.0

Uranium binding site 5 out of 15 in 6bjy

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Uranium binding site 5 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 5 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
A:U505

b:0.7
occ:1.00
OD2 A:ASP343 3.0 0.8 1.0
OE1 E:GLU253 3.1 0.1 1.0
NH2 E:ARG252 3.2 0.0 1.0
NE E:ARG252 3.4 0.7 1.0
CB E:ARG252 3.5 86.8 1.0
CG A:ASP343 3.5 0.2 1.0
CZ E:ARG252 3.7 0.1 1.0
N E:ARG252 3.7 0.6 1.0
CB A:ASP343 3.8 0.2 1.0
OE2 E:GLU253 3.9 0.1 1.0
CD E:GLU253 3.9 0.5 1.0
OE2 E:GLU323 4.1 98.0 1.0
CA E:ARG252 4.3 1.0 1.0
OD1 A:ASP343 4.4 0.7 1.0
CD E:ARG252 4.5 0.4 1.0
CG E:ARG252 4.6 98.2 1.0
C E:ASN251 4.8 0.4 1.0
NH1 E:ARG252 4.8 0.7 1.0
CA E:ASN251 4.9 82.7 1.0
N E:GLU253 5.0 0.8 1.0

Uranium binding site 6 out of 15 in 6bjy

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Uranium binding site 6 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 6 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U501

b:0.7
occ:1.00
OD2 B:ASP123 3.8 0.7 1.0
CG B:ASP123 3.9 0.6 1.0
NE2 B:GLN57 4.1 0.9 1.0
OD1 B:ASP123 4.2 0.6 1.0
CB B:ASP123 4.3 0.1 1.0
CB B:SER125 4.5 0.0 1.0
OG B:SER125 4.6 91.7 1.0
CD B:GLN57 4.8 0.8 1.0

Uranium binding site 7 out of 15 in 6bjy

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Uranium binding site 7 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 7 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U502

b:0.7
occ:1.00
OD2 C:ASP343 2.9 0.9 1.0
OE1 B:GLU323 3.2 0.6 1.0
OE2 B:GLU253 3.2 0.6 1.0
OE1 B:GLU253 3.4 0.6 1.0
O C:GLY239 3.6 93.8 1.0
CG C:ASP343 3.6 0.5 1.0
CD B:GLU253 3.7 1.0 1.0
OE2 B:GLU323 3.9 0.8 1.0
CD B:GLU323 3.9 0.4 1.0
OD1 C:ASP343 4.0 0.5 1.0
C C:GLY239 4.4 72.9 1.0
CA C:GLY239 4.5 68.3 1.0
CB B:ARG252 4.6 1.0 1.0
CB C:ASP343 4.7 0.4 1.0
CD B:ARG252 5.0 0.9 1.0

Uranium binding site 8 out of 15 in 6bjy

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Uranium binding site 8 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 8 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
B:U503

b:0.5
occ:1.00
OD1 B:ASP384 3.3 0.0 1.0
OD2 B:ASP384 3.6 0.5 1.0
CG B:ASP384 3.7 0.9 1.0
CB B:GLU383 4.9 0.3 1.0
CB B:ASP384 5.0 1.0 1.0
N B:ASP384 5.0 0.6 1.0

Uranium binding site 9 out of 15 in 6bjy

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Uranium binding site 9 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 9 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:U501

b:0.9
occ:1.00
OE1 C:GLN57 3.8 0.2 1.0
OD2 C:ASP123 4.2 0.6 1.0
CG C:ASP123 4.3 0.2 1.0
OD1 C:ASP123 4.3 0.4 1.0
CD C:GLN57 4.6 0.5 1.0
NE2 C:GLN57 4.6 0.4 1.0

Uranium binding site 10 out of 15 in 6bjy

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Uranium binding site 10 out of 15 in the Vsv Nucleocapsid with Polyamide Bound


Mono view


Stereo pair view

A full contact list of Uranium with other atoms in the U binding site number 10 of Vsv Nucleocapsid with Polyamide Bound within 5.0Å range:
probe atom residue distance (Å) B Occ
C:U502

b:0.2
occ:1.00
OE1 C:GLU323 3.2 0.3 1.0
OE2 C:GLU253 3.3 0.8 1.0
OD2 D:ASP343 3.3 0.3 1.0
CG D:ASP343 3.4 0.2 1.0
OD1 D:ASP343 3.6 0.1 1.0
OE1 C:GLU253 3.7 0.8 1.0
CD C:GLU253 3.9 0.6 1.0
OE2 C:GLU323 4.0 0.9 1.0
CD C:GLU323 4.0 0.7 1.0
O D:GLY239 4.1 0.3 1.0
CB D:ASP343 4.1 0.5 1.0
CB C:ARG252 4.4 0.8 1.0
N C:ARG252 4.8 0.1 1.0
C D:GLY239 4.9 99.2 1.0

Reference:

R.H.Gumpper, W.Li, C.H.Castaneda, M.J.Scuderi, J.K.Bashkin, M.Luo. A Polyamide Inhibits Replication of Vesicular Stomatitis Virus By Targeting Rna in the Nucleocapsid. J. Virol. V. 92 2018.
ISSN: ESSN 1098-5514
PubMed: 29437970
DOI: 10.1128/JVI.00146-18
Page generated: Wed Dec 16 02:29:59 2020

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