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Potassium in PDB 4x12: Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide

Protein crystallography data

The structure of Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide, PDB code: 4x12 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 (°) 150.210, 96.280, 128.300, 90.00, 110.28, 90.00
R / Rfree (%) 15.8 / 18.7

Potassium Binding Sites:

The binding sites of Potassium atom in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide (pdb code 4x12). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 10 binding sites of Potassium where determined in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide, PDB code: 4x12:
Jump to Potassium binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Potassium binding site 1 out of 10 in 4x12

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Potassium binding site 1 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K308

b:39.8
occ:1.00
 O B:HOH599 2.5 34.2 1.0
O B:THR205 2.7 16.7 1.0
O B:HOH486 2.7 26.0 1.0
OE2 A:GLU40 2.8 29.3 1.0
OE1 A:GLU40 2.9 31.4 1.0
CD A:GLU40 3.3 29.5 1.0
C B:THR205 3.6 17.0 1.0
CA B:THR205 4.2 15.9 1.0
N B:ARG206 4.4 15.1 1.0
NZ A:LYS279 4.6 30.8 1.0
CA B:ARG206 4.6 16.0 1.0
OH A:TYR277 4.7 18.0 1.0
CG A:GLU40 4.8 27.0 1.0
O B:PRO204 4.8 16.7 1.0
OE2 A:GLU38 4.9 40.1 1.0
CB B:THR205 4.9 18.4 1.0
O B:ARG206 5.0 14.6 1.0

Potassium binding site 2 out of 10 in 4x12

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Potassium binding site 2 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K309

b:22.1
occ:0.80
 O A:HOH605 2.4 38.5 1.0
O A:ARG161 2.7 17.3 1.0
OG1 A:THR163 2.8 19.9 1.0
O A:HOH523 2.8 26.8 1.0
O A:ASP70 2.9 15.5 1.0
O A:GLU68 2.9 21.9 1.0
OG A:SER71 3.5 22.4 0.5
N A:THR163 3.6 17.1 1.0
CB A:THR163 3.8 19.0 1.0
C A:SER69 3.8 18.5 1.0
C A:ASP70 3.9 17.0 1.0
CA A:SER69 3.9 20.2 1.0
C A:ARG161 3.9 16.5 1.0
N A:ASP70 3.9 17.5 1.0
C A:GLU68 4.0 22.7 1.0
O A:SER69 4.1 18.9 1.0
C A:THR162 4.2 16.4 1.0
CA A:THR163 4.2 16.8 1.0
CA A:THR162 4.4 15.1 1.0
N A:SER69 4.4 20.1 1.0
CA A:ASP70 4.5 16.6 1.0
N A:THR162 4.6 15.8 1.0
OE2 A:GLU68 4.7 55.0 1.0
CB A:SER71 4.7 19.6 0.5
CB A:SER71 4.7 20.1 0.5
O A:HOH557 4.8 42.1 1.0
O A:HOH589 4.8 37.1 1.0
O A:HOH573 4.8 42.2 1.0
N A:SER71 4.8 17.4 1.0
CA A:SER71 5.0 18.2 0.5
CA A:SER71 5.0 18.4 0.5

Potassium binding site 3 out of 10 in 4x12

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Potassium binding site 3 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:K310

b:30.4
occ:0.50
 O A:HOH487 2.4 36.9 1.0
O A:HOH414 2.5 27.4 1.0
O E:HOH568 2.6 42.2 1.0
O A:THR205 2.9 19.8 1.0
OE2 E:GLU40 2.9 34.0 1.0
OE1 E:GLU40 3.2 36.6 1.0
CD E:GLU40 3.5 33.9 1.0
C A:THR205 3.7 17.7 1.0
CA A:THR205 4.3 17.4 1.0
N A:ARG206 4.5 16.7 1.0
OH E:TYR277 4.6 18.9 1.0
CA A:ARG206 4.7 17.1 1.0
O A:PRO204 4.8 17.4 1.0
CD E:LYS279 4.8 32.5 1.0
O A:ARG206 4.9 14.8 1.0
CG E:GLU40 4.9 29.1 1.0

Potassium binding site 4 out of 10 in 4x12

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Potassium binding site 4 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K308

b:33.2
occ:1.00
 O C:HOH566 2.3 35.8 1.0
O B:HOH556 2.5 32.2 1.0
O C:HOH425 2.6 17.9 1.0
O C:THR205 2.7 15.3 1.0
OE2 C:GLU208 2.7 36.8 1.0
OE2 B:GLU40 2.7 27.5 1.0
OE1 B:GLU40 3.0 32.1 1.0
CD B:GLU40 3.2 28.8 1.0
C C:THR205 3.5 14.6 1.0
CD C:GLU208 3.9 35.2 1.0
CA C:THR205 4.2 14.3 1.0
N C:ARG206 4.3 13.2 1.0
CA C:ARG206 4.5 14.2 1.0
NZ B:LYS279 4.5 29.5 1.0
CG C:GLU208 4.5 29.8 1.0
OH B:TYR277 4.6 17.4 1.0
CG B:GLU40 4.7 26.7 1.0
CE B:LYS279 4.7 26.1 1.0
O C:PRO204 4.7 13.2 1.0
O C:ARG206 4.8 14.3 1.0
OE1 C:GLU208 4.8 26.9 1.0
OE2 B:GLU38 4.9 44.4 1.0
CB C:THR205 5.0 15.2 1.0

Potassium binding site 5 out of 10 in 4x12

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Potassium binding site 5 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:K309

b:21.1
occ:0.80
 O B:HOH605 2.4 40.2 1.0
O B:ARG161 2.7 17.6 1.0
OG1 B:THR163 2.8 16.4 1.0
O B:GLU68 2.9 20.2 1.0
O B:ASP70 2.9 15.4 1.0
O B:HOH568 3.0 28.4 1.0
OG B:SER71 3.6 20.8 0.5
N B:THR163 3.6 16.3 1.0
C B:SER69 3.7 18.4 1.0
CB B:THR163 3.7 17.3 1.0
CA B:SER69 3.9 19.0 1.0
C B:ASP70 3.9 16.6 1.0
C B:ARG161 3.9 15.4 1.0
N B:ASP70 3.9 17.0 1.0
C B:GLU68 3.9 20.8 1.0
O B:SER69 4.0 19.9 1.0
C B:THR162 4.2 15.1 1.0
CA B:THR163 4.3 15.9 1.0
CA B:THR162 4.3 14.0 1.0
N B:SER69 4.4 18.6 1.0
CA B:ASP70 4.5 16.3 1.0
OE2 B:GLU68 4.5 45.0 1.0
O B:HOH566 4.5 35.3 1.0
N B:THR162 4.5 14.1 1.0
CB B:SER71 4.8 18.5 0.5
N B:SER71 4.8 16.6 1.0
CB B:SER71 4.8 19.2 0.5
CD B:GLU68 4.9 38.1 1.0

Potassium binding site 6 out of 10 in 4x12

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Potassium binding site 6 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K306

b:33.1
occ:1.00
 O D:HOH587 2.4 30.5 1.0
O D:HOH561 2.5 38.9 1.0
OE2 C:GLU40 2.6 27.8 1.0
O D:HOH415 2.6 16.5 1.0
O D:THR205 2.7 15.2 1.0
OE1 C:GLU40 2.9 31.0 1.0
CD C:GLU40 3.1 28.3 1.0
C D:THR205 3.5 16.1 1.0
CA D:THR205 4.2 16.2 1.0
N D:ARG206 4.4 13.6 1.0
OH C:TYR277 4.5 17.3 1.0
CA D:ARG206 4.5 14.4 1.0
CG C:GLU40 4.6 25.1 1.0
O D:ARG206 4.8 12.9 1.0
O D:PRO204 4.8 13.8 1.0
O D:HOH588 5.0 24.5 1.0
O C:HOH585 5.0 42.0 1.0

Potassium binding site 7 out of 10 in 4x12

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Potassium binding site 7 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B 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 GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
C:K307

b:20.0
occ:0.80
 O C:GLU68 2.6 24.5 1.0
O C:HOH563 2.7 39.8 1.0
O C:ARG161 2.7 17.0 1.0
OG1 C:THR163 2.7 19.8 1.0
O C:ASP70 2.8 17.7 1.0
O C:HOH423 2.9 31.7 1.0
N C:THR163 3.6 17.5 1.0
C C:GLU68 3.6 21.1 1.0
CB C:THR163 3.7 19.4 1.0
C C:ASP70 3.8 19.1 1.0
N C:ASP70 3.8 18.0 1.0
C C:ARG161 3.9 16.6 1.0
C C:SER69 3.9 19.6 1.0
C C:THR162 4.2 17.4 1.0
CA C:SER69 4.2 20.4 1.0
CA C:THR163 4.2 18.7 1.0
N C:SER69 4.3 19.8 1.0
O C:PHE67 4.3 18.5 1.0
CA C:ASP70 4.3 18.2 1.0
O C:SER69 4.4 19.9 1.0
CA C:THR162 4.4 15.7 1.0
N C:THR162 4.6 15.5 1.0
CA C:GLU68 4.7 22.1 1.0
O C:HOH404 4.7 35.9 1.0
N C:SER71 4.8 17.9 1.0
O C:HOH558 4.8 37.4 1.0
CB C:SER71 4.9 23.5 1.0
CB C:ASP70 4.9 18.1 1.0
CA C:ARG161 5.0 16.1 1.0
CB C:ARG161 5.0 17.2 1.0

Potassium binding site 8 out of 10 in 4x12

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Potassium binding site 8 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 8 of Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K308

b:48.2
occ:1.00
 O E:HOH477 2.5 22.8 1.0
OE2 D:GLU40 2.7 25.4 1.0
O E:THR205 3.0 17.3 1.0
O D:HOH536 3.1 29.1 1.0
OE1 D:GLU40 3.4 28.8 1.0
CD D:GLU40 3.4 26.4 1.0
C E:THR205 3.7 17.1 1.0
CA E:THR205 4.3 16.7 1.0
OH D:TYR277 4.4 18.2 1.0
N E:ARG206 4.6 15.6 1.0
O E:PRO204 4.7 15.8 1.0
CA E:ARG206 4.8 16.7 1.0
CE D:LYS279 4.8 40.7 1.0
CG D:GLU40 4.8 23.6 1.0
O E:ARG206 4.9 14.5 1.0
CD D:LYS279 5.0 28.6 1.0

Potassium binding site 9 out of 10 in 4x12

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Potassium binding site 9 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 9 of Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
D:K309

b:22.0
occ:0.80
 O D:GLU68 2.6 24.1 1.0
OG1 D:THR163 2.7 21.8 1.0
O D:HOH597 2.7 43.6 1.0
O D:ARG161 2.7 19.8 1.0
O D:HOH476 2.8 32.7 1.0
O D:ASP70 2.9 17.6 1.0
N D:THR163 3.5 19.3 1.0
OG D:SER71 3.6 21.0 0.4
CB D:THR163 3.6 21.8 1.0
C D:GLU68 3.7 24.1 1.0
C D:ASP70 3.8 18.6 1.0
N D:ASP70 3.9 19.0 1.0
C D:ARG161 3.9 18.9 1.0
C D:SER69 4.0 20.7 1.0
CA D:SER69 4.2 21.8 1.0
CA D:THR163 4.2 19.2 1.0
C D:THR162 4.2 18.8 1.0
N D:SER69 4.3 21.4 1.0
CA D:THR162 4.4 17.4 1.0
CA D:ASP70 4.5 18.6 1.0
O D:SER69 4.5 21.6 1.0
N D:THR162 4.6 17.1 1.0
CA D:GLU68 4.7 26.8 1.0
N D:SER71 4.8 18.4 1.0
CB D:SER71 4.8 20.8 0.6
CB D:SER71 4.8 20.1 0.4
O D:PHE67 4.8 23.3 1.0
CA D:SER71 4.9 19.2 0.6
CA D:SER71 5.0 19.0 0.4
CG2 D:THR163 5.0 21.8 1.0

Potassium binding site 10 out of 10 in 4x12

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Potassium binding site 10 out of 10 in the Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 10 of Jc Polyomavirus Genotype 3 VP1 in Complex with GD1B Oligosaccharide within 5.0Å range:
probe atom residue distance (Å) B Occ
E:K308

b:22.0
occ:0.80
 O E:HOH407 2.6 22.8 1.0
O E:ARG161 2.7 15.8 1.0
O E:GLU68 2.7 19.4 1.0
OG1 E:THR163 2.8 20.0 1.0
O E:ASP70 2.9 16.6 1.0
O E:HOH411 3.1 44.6 1.0
OG E:SER71 3.5 27.9 1.0
N E:THR163 3.6 16.8 1.0
CB E:THR163 3.8 19.6 1.0
C E:GLU68 3.8 18.5 1.0
C E:ASP70 3.8 16.9 1.0
N E:ASP70 3.9 16.3 1.0
C E:ARG161 3.9 15.1 1.0
C E:SER69 4.1 17.2 1.0
CA E:SER69 4.2 17.4 1.0
C E:THR162 4.3 16.7 1.0
CA E:THR163 4.3 18.4 1.0
N E:SER69 4.4 17.5 1.0
CA E:THR162 4.4 14.8 1.0
CA E:ASP70 4.4 16.4 1.0
N E:THR162 4.6 14.6 1.0
O E:HOH402 4.6 28.5 1.0
O E:SER69 4.7 17.4 1.0
O E:HOH576 4.7 47.6 1.0
N E:SER71 4.7 17.4 1.0
CB E:SER71 4.7 21.5 1.0
O E:PHE67 4.7 14.5 1.0
CA E:GLU68 4.8 17.9 1.0
CA E:SER71 4.9 18.5 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: Mon Aug 12 12:22:45 2024

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