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Potassium in PDB 4x13: Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide

Protein crystallography data

The structure of Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide, PDB code: 4x13 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 / 2.00
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.120, 96.280, 128.140, 90.00, 109.81, 90.00
R / Rfree (%) 15.7 / 17.8

Potassium Binding Sites:

The binding sites of Potassium atom in the Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide (pdb code 4x13). 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 Genotype 3 VP1 in Complex with Lstc Pentasaccharide, PDB code: 4x13:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in 4x13

Go back to Potassium Binding Sites List in 4x13
Potassium binding site 1 out of 5 in the Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide


Mono view


Stereo pair view

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

b:18.9
occ:0.80
 O A:ARG161 2.6 22.1 1.0
O A:HOH538 2.7 38.0 1.0
OG1 A:THR163 2.8 23.1 1.0
O A:GLU68 2.8 30.4 1.0
O A:ASP70 2.9 20.8 1.0
O A:HOH497 2.9 33.4 1.0
N A:THR163 3.5 21.2 1.0
CB A:THR163 3.7 22.6 1.0
C A:ASP70 3.8 22.1 1.0
C A:ARG161 3.8 20.9 1.0
C A:SER69 3.8 24.6 1.0
N A:ASP70 3.9 23.2 1.0
C A:GLU68 3.9 29.1 1.0
CA A:SER69 4.0 26.2 1.0
C A:THR162 4.1 20.7 1.0
CA A:THR163 4.2 21.6 1.0
O A:SER69 4.3 25.1 1.0
CA A:THR162 4.3 19.7 1.0
N A:SER69 4.4 26.9 1.0
CA A:ASP70 4.4 21.2 1.0
O A:HOH537 4.5 41.2 1.0
N A:THR162 4.5 19.8 1.0
OE2 A:GLU68 4.6 50.9 1.0
O A:HOH496 4.7 35.1 1.0
CB A:SER71 4.7 26.0 1.0
N A:SER71 4.8 22.5 1.0
CA A:ARG161 4.9 21.0 1.0
CD A:GLU68 5.0 46.7 1.0
OG A:SER71 5.0 30.8 1.0
CA A:SER71 5.0 23.7 1.0

Potassium binding site 2 out of 5 in 4x13

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Potassium binding site 2 out of 5 in the Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K314

b:28.1
occ:1.00
 OG1 B:THR163 2.7 20.5 1.0
O B:GLU68 2.7 24.4 1.0
O B:ARG161 2.8 20.4 1.0
O B:ASP70 2.9 19.4 1.0
O B:HOH415 2.9 41.6 1.0
OG B:SER71 3.4 30.0 1.0
N B:THR163 3.6 19.5 1.0
CB B:THR163 3.6 21.5 1.0
C B:ASP70 3.7 20.7 1.0
C B:GLU68 3.8 23.9 1.0
N B:ASP70 4.0 21.7 1.0
C B:ARG161 4.0 19.8 1.0
C B:SER69 4.1 22.0 1.0
CA B:THR163 4.2 20.4 1.0
C B:THR162 4.2 19.8 1.0
CA B:SER69 4.3 22.6 1.0
CA B:THR162 4.4 18.5 1.0
CA B:ASP70 4.4 20.1 1.0
N B:SER69 4.4 23.0 1.0
N B:SER71 4.6 21.9 1.0
CB B:SER71 4.6 24.0 1.0
O B:SER69 4.7 22.5 1.0
N B:THR162 4.7 18.1 1.0
CA B:SER71 4.7 22.9 1.0
O B:PHE67 4.8 20.8 1.0
CA B:GLU68 4.8 23.8 1.0
CG2 B:THR163 4.9 21.7 1.0

Potassium binding site 3 out of 5 in 4x13

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Potassium binding site 3 out of 5 in the Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K310

b:21.6
occ:0.80
 O C:HOH585 2.6 36.9 1.0
O C:ARG161 2.7 19.1 1.0
OG1 C:THR163 2.8 20.8 1.0
O C:HOH506 2.8 24.7 1.0
O C:GLU68 2.8 22.4 1.0
O C:ASP70 2.9 18.9 1.0
OG C:SER71 3.6 21.0 0.5
N C:THR163 3.6 18.6 1.0
C C:SER69 3.7 20.4 1.0
C C:ASP70 3.8 19.3 1.0
CB C:THR163 3.8 19.9 1.0
N C:ASP70 3.9 19.1 1.0
C C:ARG161 3.9 18.9 1.0
C C:GLU68 3.9 22.8 1.0
CA C:SER69 3.9 21.0 1.0
O C:SER69 4.1 21.3 1.0
C C:THR162 4.2 18.0 1.0
CA C:THR163 4.3 18.6 1.0
CA C:THR162 4.4 17.4 1.0
N C:SER69 4.4 21.1 1.0
CA C:ASP70 4.4 18.5 1.0
O C:HOH560 4.5 45.2 1.0
OE2 C:GLU68 4.5 45.0 1.0
N C:THR162 4.6 17.4 1.0
CB C:SER71 4.8 20.8 0.5
N C:SER71 4.8 19.2 1.0
CB C:SER71 4.8 21.0 0.5
CD C:GLU68 4.9 39.3 1.0
CA C:ARG161 5.0 19.2 1.0

Potassium binding site 4 out of 5 in 4x13

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Potassium binding site 4 out of 5 in the Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K305

b:25.5
occ:1.00
 O D:HOH602 2.5 39.3 1.0
O D:ARG161 2.7 20.4 1.0
O D:GLU68 2.8 25.3 1.0
OG1 D:THR163 2.8 20.2 1.0
O D:HOH494 2.9 28.8 1.0
O D:ASP70 3.0 18.1 1.0
OG D:SER71 3.6 20.4 0.4
N D:THR163 3.6 19.1 1.0
C D:SER69 3.7 21.2 1.0
CB D:THR163 3.8 20.4 1.0
CA D:SER69 3.8 22.6 1.0
C D:ARG161 3.8 18.7 1.0
C D:GLU68 3.9 23.9 1.0
N D:ASP70 3.9 20.2 1.0
C D:ASP70 3.9 19.4 1.0
O D:SER69 4.0 21.6 1.0
C D:THR162 4.2 18.8 1.0
N D:SER69 4.3 22.9 1.0
CA D:THR163 4.3 19.4 1.0
OE2 D:GLU68 4.3 41.7 1.0
CA D:THR162 4.4 17.8 1.0
CA D:ASP70 4.5 18.8 1.0
N D:THR162 4.5 17.5 1.0
CB D:SER71 4.8 21.2 0.6
CD D:GLU68 4.8 38.9 1.0
N D:SER71 4.9 18.9 1.0
CB D:SER71 4.9 20.5 0.4
O D:HOH589 4.9 41.2 1.0
CA D:ARG161 4.9 19.0 1.0
CB D:ARG161 5.0 19.6 1.0

Potassium binding site 5 out of 5 in 4x13

Go back to Potassium Binding Sites List in 4x13
Potassium binding site 5 out of 5 in the Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Jc Polyomavirus Genotype 3 VP1 in Complex with Lstc Pentasaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K310

b:25.5
occ:0.80
 O E:GLU68 2.6 31.1 1.0
OG1 E:THR163 2.7 26.3 1.0
O E:ARG161 2.8 20.6 1.0
O E:ASP70 2.9 25.5 1.0
O E:HOH417 3.0 38.1 1.0
N E:THR163 3.6 22.4 1.0
CB E:THR163 3.7 25.3 1.0
C E:GLU68 3.7 30.9 1.0
C E:ASP70 3.8 24.8 1.0
N E:ASP70 3.8 24.6 1.0
C E:SER69 3.9 26.0 1.0
C E:ARG161 4.0 20.0 1.0
CA E:SER69 4.1 27.0 1.0
CA E:THR163 4.2 23.3 1.0
C E:THR162 4.3 20.7 1.0
N E:SER69 4.3 27.8 1.0
O E:SER69 4.4 26.8 1.0
CA E:ASP70 4.4 23.4 1.0
CA E:THR162 4.5 19.4 1.0
OE1 E:GLU68 4.5 63.4 1.0
O E:PHE67 4.7 28.3 1.0
N E:THR162 4.7 18.7 1.0
N E:SER71 4.8 22.7 1.0
CB E:SER71 4.8 28.3 1.0
CA E:GLU68 4.8 33.4 1.0
OG E:SER71 5.0 33.7 1.0
CB E:ASP70 5.0 21.6 1.0
O E:HOH409 5.0 35.0 1.0
CG2 E:THR163 5.0 27.4 1.0
CD E:GLU68 5.0 53.8 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: Mon Aug 12 12:24:45 2024

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