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Potassium in PDB 4x0y: Jc Polyomavirus VP1 From A Genotype 3 Strain

Protein crystallography data

The structure of Jc Polyomavirus VP1 From A Genotype 3 Strain, PDB code: 4x0y was solved by L.J.Stroh, T.Stehle, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.00 / 1.70
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.480, 96.830, 128.220, 90.00, 110.55, 90.00
R / Rfree (%) 15.7 / 17.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Jc Polyomavirus VP1 From A Genotype 3 Strain (pdb code 4x0y). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 5 binding sites of Potassium where determined in the Jc Polyomavirus VP1 From A Genotype 3 Strain, PDB code: 4x0y:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 4x0y

Go back to Potassium Binding Sites List in 4x0y
Potassium binding site 1 out of 5 in the Jc Polyomavirus VP1 From A Genotype 3 Strain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Jc Polyomavirus VP1 From A Genotype 3 Strain within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K306

b:22.7
occ:1.00
 O A:ARG161 2.7 17.0 1.0
O A:GLU68 2.7 23.0 1.0
O A:HOH406 2.7 28.5 1.0
OG1 A:THR163 2.8 19.6 1.0
O A:ASP70 2.9 17.8 1.0
O A:HOH407 2.9 41.1 1.0
N A:THR163 3.6 16.8 1.0
OG A:SER71 3.7 19.9 0.5
CB A:THR163 3.8 18.8 1.0
C A:GLU68 3.8 23.0 1.0
C A:ASP70 3.8 18.1 1.0
C A:ARG161 3.9 16.2 1.0
N A:ASP70 3.9 18.3 1.0
C A:SER69 4.0 19.9 1.0
C A:THR162 4.2 16.5 1.0
CA A:THR163 4.2 17.4 1.0
CA A:SER69 4.2 21.4 1.0
CA A:THR162 4.4 15.1 1.0
N A:SER69 4.4 21.1 1.0
CA A:ASP70 4.5 17.3 1.0
O A:SER69 4.5 20.8 1.0
O A:HOH615 4.6 41.6 1.0
N A:THR162 4.6 15.5 1.0
OE2 A:GLU68 4.7 50.2 1.0
N A:SER71 4.8 17.1 1.0
O A:HOH571 4.8 39.9 1.0
O A:PHE67 4.8 19.3 1.0
CB A:SER71 4.8 18.4 0.5
CA A:GLU68 4.9 24.8 1.0
CB A:SER71 4.9 18.7 0.5
O A:HOH590 4.9 42.6 1.0
CA A:ARG161 5.0 16.8 1.0

Potassium binding site 2 out of 5 in 4x0y

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Potassium binding site 2 out of 5 in the Jc Polyomavirus VP1 From A Genotype 3 Strain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Jc Polyomavirus VP1 From A Genotype 3 Strain within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K306

b:22.3
occ:1.00
 O B:HOH486 2.6 38.6 1.0
O B:ARG161 2.7 16.0 1.0
O B:GLU68 2.7 22.2 1.0
O B:HOH622 2.7 29.7 1.0
OG1 B:THR163 2.8 18.3 1.0
O B:ASP70 2.9 17.0 1.0
OG B:SER71 3.5 23.7 0.5
N B:THR163 3.6 16.9 1.0
CB B:THR163 3.7 18.9 1.0
C B:GLU68 3.8 22.1 1.0
C B:ASP70 3.8 17.7 1.0
N B:ASP70 3.9 17.8 1.0
C B:ARG161 3.9 15.7 1.0
C B:SER69 4.0 19.6 1.0
C B:THR162 4.2 15.5 1.0
CA B:THR163 4.2 17.4 1.0
CA B:SER69 4.2 20.6 1.0
CA B:THR162 4.4 14.8 1.0
O B:HOH536 4.4 41.2 1.0
N B:SER69 4.4 21.1 1.0
CA B:ASP70 4.4 17.1 1.0
O B:SER69 4.5 21.3 1.0
N B:THR162 4.6 15.2 1.0
OE2 B:GLU68 4.7 49.7 1.0
O B:PHE67 4.7 18.8 1.0
CB B:SER71 4.7 20.4 0.5
CB B:SER71 4.7 20.9 0.5
N B:SER71 4.8 17.4 1.0
CA B:GLU68 4.9 23.9 1.0
CA B:SER71 5.0 18.2 0.5
CA B:SER71 5.0 18.4 0.5
CA B:ARG161 5.0 16.0 1.0
CD B:GLU68 5.0 38.2 1.0

Potassium binding site 3 out of 5 in 4x0y

Go back to Potassium Binding Sites List in 4x0y
Potassium binding site 3 out of 5 in the Jc Polyomavirus VP1 From A Genotype 3 Strain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Jc Polyomavirus VP1 From A Genotype 3 Strain within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K305

b:20.8
occ:1.00
 O C:ARG161 2.7 13.6 1.0
O C:HOH577 2.7 38.5 1.0
O C:GLU68 2.7 16.2 1.0
OG1 C:THR163 2.7 17.1 1.0
O C:HOH419 2.7 30.9 1.0
O C:ASP70 2.9 13.6 1.0
N C:THR163 3.6 15.3 1.0
OG C:SER71 3.7 20.4 0.5
CB C:THR163 3.7 16.6 1.0
C C:GLU68 3.7 16.2 1.0
C C:ASP70 3.8 14.5 1.0
N C:ASP70 3.8 13.5 1.0
C C:ARG161 3.9 13.3 1.0
C C:SER69 4.0 15.0 1.0
C C:THR162 4.2 14.3 1.0
CA C:THR163 4.2 15.5 1.0
CA C:SER69 4.3 15.7 1.0
CA C:ASP70 4.4 13.6 1.0
N C:SER69 4.4 15.4 1.0
CA C:THR162 4.4 12.8 1.0
O C:SER69 4.5 15.7 1.0
O C:PHE67 4.6 14.1 1.0
N C:THR162 4.6 12.3 1.0
OE1 C:GLU68 4.7 49.6 1.0
N C:SER71 4.8 14.0 1.0
CA C:GLU68 4.8 16.9 1.0
O C:HOH412 4.8 31.1 1.0
CB C:SER71 4.9 15.8 0.5
CB C:SER71 4.9 17.2 0.5
O C:HOH554 4.9 37.0 1.0
CB C:ASP70 4.9 13.5 1.0
CD C:GLU68 4.9 32.6 1.0
CA C:ARG161 5.0 13.9 1.0

Potassium binding site 4 out of 5 in 4x0y

Go back to Potassium Binding Sites List in 4x0y
Potassium binding site 4 out of 5 in the Jc Polyomavirus VP1 From A Genotype 3 Strain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Jc Polyomavirus VP1 From A Genotype 3 Strain within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K307

b:21.6
occ:1.00
 O D:ARG161 2.6 15.2 1.0
O D:GLU68 2.7 21.3 1.0
O D:HOH1255 2.7 29.0 1.0
O D:HOH1237 2.8 36.5 1.0
OG1 D:THR163 2.8 19.6 1.0
O D:ASP70 2.9 16.5 1.0
OG D:SER71 3.6 20.2 0.5
N D:THR163 3.6 16.4 1.0
CB D:THR163 3.7 19.0 1.0
C D:GLU68 3.8 20.9 1.0
C D:ASP70 3.8 17.1 1.0
C D:ARG161 3.9 15.3 1.0
N D:ASP70 3.9 16.6 1.0
C D:SER69 4.0 18.2 1.0
C D:THR162 4.2 16.2 1.0
CA D:SER69 4.2 19.3 1.0
CA D:THR163 4.3 17.0 1.0
CA D:THR162 4.4 15.2 1.0
N D:SER69 4.4 18.9 1.0
CA D:ASP70 4.4 16.3 1.0
O D:SER69 4.5 19.9 1.0
N D:THR162 4.6 15.1 1.0
OE1 D:GLU68 4.7 44.2 1.0
O D:PHE67 4.8 19.4 1.0
N D:SER71 4.8 17.1 1.0
CA D:GLU68 4.8 22.4 1.0
CB D:SER71 4.8 18.5 0.5
CB D:SER71 4.8 18.5 0.5
O D:HOH1233 4.9 35.8 1.0
CA D:ARG161 5.0 15.1 1.0
CD D:GLU68 5.0 34.4 1.0

Potassium binding site 5 out of 5 in 4x0y

Go back to Potassium Binding Sites List in 4x0y
Potassium binding site 5 out of 5 in the Jc Polyomavirus VP1 From A Genotype 3 Strain


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Jc Polyomavirus VP1 From A Genotype 3 Strain within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K305

b:23.2
occ:1.00
 O E:HOH410 2.6 26.3 1.0
O E:ARG161 2.7 13.2 1.0
OG1 E:THR163 2.7 16.8 1.0
O E:GLU68 2.8 17.9 1.0
O E:HOH411 2.9 35.8 1.0
O E:ASP70 2.9 15.3 1.0
OG E:SER71 3.3 15.5 0.5
N E:THR163 3.6 13.9 1.0
CB E:THR163 3.6 15.9 1.0
C E:ASP70 3.8 15.1 1.0
O E:HOH409 3.8 43.1 1.0
C E:GLU68 3.8 16.1 1.0
N E:ASP70 3.9 13.3 1.0
C E:ARG161 3.9 12.8 1.0
C E:SER69 4.0 14.6 1.0
CA E:THR163 4.2 14.7 1.0
CA E:SER69 4.2 14.8 1.0
C E:THR162 4.2 13.5 1.0
CA E:THR162 4.4 12.6 1.0
N E:SER69 4.4 15.2 1.0
CA E:ASP70 4.4 13.7 1.0
N E:THR162 4.6 12.2 1.0
CB E:SER71 4.6 16.1 0.5
N E:SER71 4.6 14.9 1.0
O E:SER69 4.6 14.6 1.0
CB E:SER71 4.6 17.2 0.5
O E:HOH408 4.6 27.6 1.0
O E:HOH577 4.8 39.3 1.0
O E:PHE67 4.8 12.5 1.0
CA E:SER71 4.8 14.6 0.5
CA E:SER71 4.8 15.1 0.5
CA E:GLU68 4.9 15.4 1.0
CG2 E:THR163 5.0 17.5 1.0

Reference:

L.J.Stroh, M.S.Maginnis, B.S.Blaum, C.D.Nelson, U.Neu, G.V.Gee, B.A.O'hara, N.Motamedi, D.Dimaio, W.J.Atwood, T.Stehle. The Greater Affinity of Jc Polyomavirus Capsid For Alpha 2,6-Linked Lactoseries Tetrasaccharide C Than For Other Sialylated Glycans Is A Major Determinant of Infectivity. J.Virol. V. 89 6364 2015.
ISSN: ESSN 1098-5514
PubMed: 25855729
DOI: 10.1128/JVI.00489-15
Page generated: Sun Dec 13 23:50:26 2020

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