Atomistry » Potassium » PDB 4wpz-4xs4 » 4x10
Atomistry »
  Potassium »
    PDB 4wpz-4xs4 »
      4x10 »

Potassium in PDB 4x10: Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide

Protein crystallography data

The structure of Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide, PDB code: 4x10 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 / 1.90
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 150.410, 96.060, 128.750, 90.00, 110.21, 90.00
R / Rfree (%) 16.4 / 19.6

Potassium Binding Sites:

The binding sites of Potassium atom in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide (pdb code 4x10). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 7 binding sites of Potassium where determined in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide, PDB code: 4x10:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7;

Potassium binding site 1 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 1 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


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 GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K305

b:27.2
occ:0.80
 O A:GLU68 2.7 37.5 1.0
O A:HOH607 2.7 35.2 1.0
O A:ARG161 2.7 24.8 1.0
O A:HOH553 2.8 47.2 1.0
OG1 A:THR163 2.8 30.0 1.0
O A:ASP70 2.9 21.6 1.0
N A:THR163 3.6 23.2 1.0
CB A:THR163 3.7 27.4 1.0
C A:GLU68 3.7 37.1 1.0
C A:ASP70 3.9 23.8 1.0
N A:ASP70 3.9 24.0 1.0
C A:ARG161 3.9 23.2 1.0
C A:SER69 3.9 25.0 1.0
CA A:SER69 4.1 26.4 1.0
CA A:THR163 4.2 24.9 1.0
C A:THR162 4.2 23.9 1.0
OE1 A:GLU68 4.3 64.8 1.0
N A:SER69 4.3 25.6 1.0
CA A:THR162 4.4 22.4 1.0
O A:SER69 4.4 26.7 1.0
CA A:ASP70 4.5 22.6 1.0
N A:THR162 4.6 22.4 1.0
CB A:SER71 4.7 28.3 1.0
CA A:GLU68 4.9 40.3 1.0
N A:SER71 4.9 24.1 1.0
O A:PHE67 4.9 35.3 1.0
O A:HOH601 4.9 43.5 1.0
CA A:ARG161 5.0 22.9 1.0

Potassium binding site 2 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 2 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


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 GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K306

b:30.9
occ:1.00
 O A:HOH523 2.4 36.4 1.0
O A:HOH593 2.4 32.8 1.0
O A:HOH530 2.6 18.7 1.0
OE2 E:GLU40 2.6 29.1 1.0
O A:THR205 2.7 17.7 1.0
O A:HOH486 2.8 42.7 1.0
OE1 E:GLU40 3.0 33.6 1.0
CD E:GLU40 3.2 30.0 1.0
C A:THR205 3.5 19.8 1.0
CA A:THR205 4.2 19.2 1.0
OE1 A:GLU208 4.3 56.5 1.0
N A:ARG206 4.4 17.2 1.0
CD A:GLU208 4.4 48.4 1.0
OH E:TYR277 4.5 20.2 1.0
CA A:ARG206 4.5 18.6 1.0
CG A:GLU208 4.5 35.2 1.0
O E:HOH479 4.5 32.4 1.0
CG E:GLU40 4.7 27.6 1.0
O A:ARG206 4.8 16.6 1.0
O A:PRO204 4.9 16.1 1.0
OE2 A:GLU208 5.0 49.1 1.0
O A:HOH511 5.0 29.8 1.0

Potassium binding site 3 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 3 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


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 GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K310

b:24.2
occ:0.80
 OG1 B:THR163 2.6 23.2 1.0
O B:GLU68 2.6 22.6 1.0
O B:ARG161 2.7 21.7 1.0
O B:HOH568 2.8 39.8 1.0
O B:ASP70 2.9 20.7 1.0
O B:HOH547 3.0 43.9 1.0
OG B:SER71 3.4 36.4 1.0
N B:THR163 3.6 21.5 1.0
CB B:THR163 3.6 25.3 1.0
C B:GLU68 3.7 23.8 1.0
C B:ASP70 3.9 21.0 1.0
C B:ARG161 4.0 21.0 1.0
N B:ASP70 4.0 19.3 1.0
C B:SER69 4.1 21.9 1.0
CA B:THR163 4.2 23.2 1.0
C B:THR162 4.2 22.6 1.0
CA B:SER69 4.3 21.7 1.0
N B:SER69 4.4 21.7 1.0
CA B:THR162 4.4 20.2 1.0
CA B:ASP70 4.6 19.8 1.0
CB B:SER71 4.7 27.5 1.0
N B:THR162 4.7 19.9 1.0
CA B:GLU68 4.7 24.5 1.0
O B:SER69 4.7 22.7 1.0
O B:HOH499 4.7 26.7 1.0
N B:SER71 4.7 22.0 1.0
CA B:SER71 4.8 24.2 1.0
O B:HOH584 4.9 42.6 1.0
O B:PHE67 4.9 19.4 1.0
CG2 B:THR163 4.9 26.8 1.0

Potassium binding site 4 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 4 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


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 GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K309

b:27.1
occ:0.80
 O C:HOH514 2.5 40.7 1.0
O C:ARG161 2.7 20.2 1.0
OG1 C:THR163 2.8 23.3 1.0
O C:GLU68 2.9 21.9 1.0
O C:HOH592 2.9 28.4 1.0
O C:ASP70 2.9 18.8 1.0
OG C:SER71 3.6 23.6 0.5
N C:THR163 3.6 20.5 1.0
C C:SER69 3.8 20.9 1.0
CB C:THR163 3.8 22.1 1.0
CA C:SER69 3.9 21.4 1.0
C C:ARG161 3.9 20.9 1.0
C C:ASP70 3.9 19.6 1.0
C C:GLU68 3.9 22.9 1.0
N C:ASP70 4.0 20.2 1.0
O C:SER69 4.1 21.7 1.0
C C:THR162 4.2 19.9 1.0
CA C:THR163 4.3 20.3 1.0
N C:SER69 4.4 21.3 1.0
CA C:THR162 4.4 18.5 1.0
CA C:ASP70 4.6 19.2 1.0
O C:HOH503 4.6 41.3 1.0
N C:THR162 4.6 18.6 1.0
OE2 C:GLU68 4.6 50.6 1.0
O C:HOH431 4.8 40.4 1.0
CB C:SER71 4.8 20.8 0.5
CB C:SER71 4.8 21.9 0.5
N C:SER71 4.9 19.9 1.0

Potassium binding site 5 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 5 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


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 GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K308

b:27.2
occ:0.80
 O D:ARG161 2.7 19.7 1.0
OG1 D:THR163 2.8 21.5 1.0
O D:GLU68 2.9 23.1 1.0
O D:ASP70 2.9 18.0 1.0
O D:HOH559 2.9 29.5 1.0
OG D:SER71 3.5 22.2 0.4
N D:THR163 3.6 20.1 1.0
C D:SER69 3.7 20.6 1.0
CB D:THR163 3.7 22.2 1.0
CA D:SER69 3.8 21.4 1.0
C D:ASP70 3.9 19.8 1.0
C D:ARG161 3.9 18.8 1.0
C D:GLU68 3.9 22.8 1.0
N D:ASP70 3.9 20.0 1.0
O D:SER69 4.0 20.2 1.0
C D:THR162 4.2 19.6 1.0
CA D:THR163 4.2 21.1 1.0
N D:SER69 4.3 21.8 1.0
CA D:THR162 4.4 17.9 1.0
O D:HOH440 4.4 41.9 1.0
CA D:ASP70 4.5 19.4 1.0
OE2 D:GLU68 4.5 50.2 1.0
N D:THR162 4.6 17.1 1.0
CB D:SER71 4.7 21.4 0.6
CB D:SER71 4.8 21.5 0.4
N D:SER71 4.8 19.7 1.0

Potassium binding site 6 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 6 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 6 of Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K309

b:26.6
occ:0.80
 O E:HOH480 2.3 30.7 1.0
O E:HOH574 2.3 33.2 1.0
O E:HOH510 2.3 37.1 1.0
OE2 D:GLU40 2.6 27.3 1.0
O E:HOH449 2.6 48.9 1.0
O E:HOH491 2.7 21.1 1.0
O E:THR205 2.7 18.2 1.0
OE1 D:GLU40 2.8 31.2 1.0
CD D:GLU40 3.1 29.4 1.0
C E:THR205 3.6 18.0 1.0
OE1 E:GLU208 3.7 52.8 1.0
CA E:THR205 4.3 16.8 1.0
N E:ARG206 4.4 16.8 1.0
CD E:GLU208 4.5 54.0 1.0
OH D:TYR277 4.5 20.1 1.0
CG E:GLU208 4.5 36.8 1.0
CA E:ARG206 4.6 16.9 1.0
CG D:GLU40 4.6 28.6 1.0
O D:HOH497 4.6 35.1 1.0
O E:ARG206 4.8 16.7 1.0
O E:PRO204 4.8 16.1 1.0

Potassium binding site 7 out of 7 in 4x10

Go back to Potassium Binding Sites List in 4x10
Potassium binding site 7 out of 7 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 7 of Jc Polyomavirus Genotype 3 VP1 in Complex with GM2 Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K305

b:29.4
occ:0.80
 O E:HOH531 2.6 42.8 1.0
OG1 E:THR163 2.7 23.5 1.0
O E:ARG161 2.8 22.3 1.0
O E:ASP70 2.9 22.7 1.0
O E:GLU68 2.9 31.8 1.0
O E:HOH505 3.0 34.7 1.0
OG E:SER71 3.5 29.8 0.5
N E:THR163 3.6 21.7 1.0
CB E:THR163 3.7 23.4 1.0
C E:SER69 3.8 23.3 1.0
C E:ASP70 3.9 23.7 1.0
C E:ARG161 3.9 20.9 1.0
C E:GLU68 4.0 30.5 1.0
N E:ASP70 4.0 23.0 1.0
CA E:SER69 4.0 24.8 1.0
O E:SER69 4.1 25.0 1.0
C E:THR162 4.2 20.1 1.0
CA E:THR163 4.2 22.1 1.0
CA E:THR162 4.4 19.5 1.0
N E:SER69 4.4 26.0 1.0
CA E:ASP70 4.5 22.4 1.0
OE2 E:GLU68 4.6 64.0 1.0
N E:THR162 4.6 19.5 1.0
CB E:SER71 4.7 23.7 0.5
CB E:SER71 4.8 25.2 0.5
O E:HOH416 4.8 39.9 1.0
N E:SER71 4.8 22.1 1.0
O E:THR162 5.0 19.9 1.0
CG2 E:THR163 5.0 24.9 1.0
CA E:SER71 5.0 22.1 0.5
CA E:SER71 5.0 22.9 0.5
CD E:GLU68 5.0 51.8 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 12:22:32 2024

Last articles

Zn in 9JYW
Zn in 9IR4
Zn in 9IR3
Zn in 9GMX
Zn in 9GMW
Zn in 9JEJ
Zn in 9ERF
Zn in 9ERE
Zn in 9EGV
Zn in 9EGW
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy