Potassium in PDB 4x14: Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide

The structure of Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide, PDB code: 4x14 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 / 2.30
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	150.450, 95.590, 129.670, 90.00, 110.17, 90.00
R / Rfree (%)	18.7 / 21.1

The binding sites of Potassium atom in the Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide (pdb code 4x14). 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 Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide, PDB code: 4x14:
Jump to Potassium binding site number: 1; 2; 3; 4; 5;

Potassium binding site 1 out of 5 in the Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 1 of Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:K306 b:45.6 occ:0.80 O A:HOH516 2.5 46.9 1.0 OE1 B:GLU208 2.5 44.8 1.0 O B:HOH492 2.6 33.7 1.0 O B:THR205 2.7 28.7 1.0 OE2 A:GLU40 2.8 35.8 1.0 OE1 A:GLU40 2.9 37.0 1.0 CD A:GLU40 3.2 35.6 1.0 C B:THR205 3.6 27.9 1.0 CD B:GLU208 3.8 42.8 1.0 CA B:THR205 4.2 27.2 1.0 N B:ARG206 4.4 28.0 1.0 CA B:ARG206 4.6 28.6 1.0 CG B:GLU208 4.6 39.2 1.0 OE2 B:GLU208 4.7 43.8 1.0 OH A:TYR277 4.7 24.8 1.0 CG A:GLU40 4.7 33.9 1.0 O B:PRO204 4.9 25.4 1.0 O B:ARG206 5.0 26.9 1.0

Potassium binding site 2 out of 5 in the Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 2 of Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:K307 b:33.2 occ:0.80 OE1 A:GLU208 2.4 34.9 1.0 OE2 E:GLU40 2.5 36.0 1.0 O A:HOH510 2.6 40.4 1.0 O A:THR205 2.6 25.5 1.0 OE1 E:GLU40 2.6 36.9 1.0 O A:HOH515 2.7 32.0 1.0 O A:HOH493 2.7 24.1 1.0 O A:HOH507 2.8 40.6 1.0 CD E:GLU40 2.9 34.9 1.0 C A:THR205 3.6 24.7 1.0 CD A:GLU208 3.7 33.6 1.0 CA A:THR205 4.3 24.6 1.0 N A:ARG206 4.4 24.8 1.0 CG E:GLU40 4.4 32.0 1.0 CG A:GLU208 4.5 30.9 1.0 CA A:ARG206 4.5 25.1 1.0 OE2 A:GLU208 4.5 34.6 1.0 OH E:TYR277 4.6 23.5 1.0 O A:ARG206 4.9 23.8 1.0

Potassium binding site 3 out of 5 in the Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 3 of Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:K309 b:42.0 occ:0.80 O C:HOH474 2.5 33.4 1.0 O B:HOH524 2.8 33.9 1.0 O C:THR205 2.9 28.3 1.0 OE2 B:GLU40 2.9 38.0 1.0 OE1 B:GLU40 3.0 39.4 1.0 OE2 C:GLU208 3.1 39.3 1.0 CD B:GLU40 3.3 37.5 1.0 C C:THR205 3.6 28.1 1.0 CD C:GLU208 4.3 38.4 1.0 CA C:THR205 4.3 27.5 1.0 N C:ARG206 4.4 28.6 1.0 CA C:ARG206 4.5 29.1 1.0 OH B:TYR277 4.8 26.4 1.0 CG B:GLU40 4.9 35.4 1.0 OE1 C:GLU208 4.9 39.1 1.0 O C:ARG206 4.9 27.5 1.0 O C:PRO204 4.9 26.9 1.0

Potassium binding site 4 out of 5 in the Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 4 of Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ C:K310 b:37.5 occ:0.80 OE2 D:GLU208 2.4 37.6 1.0 O D:HOH619 2.6 43.8 1.0 O D:THR205 2.6 26.8 1.0 O D:HOH522 2.7 21.6 1.0 OE2 C:GLU40 2.7 37.8 1.0 OE1 C:GLU40 2.8 37.0 1.0 CD C:GLU40 3.1 36.2 1.0 C D:THR205 3.5 25.8 1.0 CD D:GLU208 3.7 35.9 1.0 O D:HOH565 4.2 40.9 1.0 CA D:THR205 4.3 25.4 1.0 N D:ARG206 4.4 26.1 1.0 CG D:GLU208 4.4 33.4 1.0 CA D:ARG206 4.5 26.2 1.0 OE1 D:GLU208 4.6 36.8 1.0 OH C:TYR277 4.6 21.3 1.0 CG C:GLU40 4.6 34.4 1.0 O D:PRO204 4.8 23.6 1.0 O D:ARG206 4.8 24.6 1.0

Potassium binding site 5 out of 5 in the Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide


Mono view


Stereo pair view

A full contact list of Potassium with other atoms in the K binding site number 5 of Jc Mad-1 Polyomavirus VP1 in Complex with GM1 Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:K309 b:30.9 occ:0.80 O E:HOH501 2.5 32.9 1.0 OE2 D:GLU40 2.5 33.8 1.0 O E:HOH489 2.5 20.0 1.0 OE2 E:GLU208 2.6 35.8 1.0 O E:THR205 2.6 24.0 1.0 OE1 D:GLU40 2.7 33.1 1.0 CD D:GLU40 3.0 32.4 1.0 C E:THR205 3.5 23.3 1.0 CD E:GLU208 3.8 33.9 1.0 CA E:THR205 4.2 22.8 1.0 O E:HOH493 4.3 34.5 1.0 N E:ARG206 4.3 23.2 1.0 CG D:GLU40 4.5 30.6 1.0 CA E:ARG206 4.5 23.7 1.0 OH D:TYR277 4.5 21.2 1.0 CG E:GLU208 4.5 30.8 1.0 OE1 E:GLU208 4.7 36.1 1.0 O E:PRO204 4.8 20.8 1.0 O E:ARG206 4.8 22.1 1.0 O D:HOH613 4.9 36.3 1.0 CB E:THR205 4.9 23.5 1.0

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