Potassium in PDB 4x16: Jc Mad-1 Polyomavirus VP1 in Complex with GD1A Oligosaccharide

The structure of Jc Mad-1 Polyomavirus VP1 in Complex with GD1A Oligosaccharide, PDB code: 4x16 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 / 1.80
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.810, 95.580, 128.790, 90.00, 110.33, 90.00
R / Rfree (%)	16.6 / 19.1

The binding sites of Potassium atom in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1A Oligosaccharide (pdb code 4x16). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 3 binding sites of Potassium where determined in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1A Oligosaccharide, PDB code: 4x16:
Jump to Potassium binding site number: 1; 2; 3;

Potassium binding site 1 out of 3 in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1A 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 GD1A Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:K303 b:37.5 occ:0.50 O B:HOH438 2.5 28.7 1.0 O A:HOH514 2.7 31.0 1.0 O B:THR205 2.9 19.5 1.0 OE2 A:GLU40 2.9 29.9 1.0 OE1 A:GLU40 3.2 31.1 1.0 CD A:GLU40 3.4 29.2 1.0 C B:THR205 3.7 19.0 1.0 CA B:THR205 4.3 18.6 1.0 NZ A:LYS279 4.5 23.1 1.0 N B:ARG206 4.6 19.0 1.0 OH A:TYR277 4.7 17.0 1.0 OE2 A:GLU38 4.7 32.5 1.0 O B:PRO204 4.9 17.6 1.0 CD A:LYS279 4.9 20.0 1.0 CG A:GLU40 4.9 26.4 1.0 CA B:ARG206 4.9 19.5 1.0

Potassium binding site 2 out of 3 in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1A 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 GD1A Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ B:K306 b:43.1 occ:0.50 O C:HOH551 2.4 37.2 1.0 O C:HOH550 2.4 44.9 1.0 OE2 B:GLU40 2.9 30.5 1.0 O C:THR205 3.0 20.1 1.0 OE1 B:GLU40 3.2 32.2 1.0 CD B:GLU40 3.5 30.3 1.0 C C:THR205 3.8 19.3 1.0 NZ B:LYS279 4.2 26.4 1.0 CA C:THR205 4.3 19.1 1.0 OE2 B:GLU38 4.6 33.3 1.0 N C:ARG206 4.7 18.6 1.0 OH B:TYR277 4.7 20.8 1.0 O C:PRO204 4.8 18.1 1.0 CD B:LYS279 4.9 23.2 1.0 CA C:ARG206 4.9 19.0 1.0 CG B:GLU40 5.0 27.9 1.0

Potassium binding site 3 out of 3 in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1A 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 GD1A Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ E:K305 b:21.8 occ:0.50 O A:HOH556 2.3 35.2 1.0 O A:HOH586 2.3 37.2 1.0 O E:HOH577 2.5 43.9 1.0 O A:HOH426 2.6 22.6 1.0 O A:THR205 2.6 17.9 1.0 OE2 E:GLU40 2.7 30.5 1.0 OE1 E:GLU40 3.1 31.8 1.0 CD E:GLU40 3.2 29.4 1.0 C A:THR205 3.5 16.9 1.0 CA A:THR205 4.2 16.5 1.0 N A:ARG206 4.4 16.8 1.0 CA A:ARG206 4.6 17.4 1.0 OH E:TYR277 4.6 17.3 1.0 CG E:GLU40 4.7 26.0 1.0 O A:PRO204 4.8 15.5 1.0 O A:ARG206 4.9 16.1 1.0 CD E:LYS279 4.9 22.3 1.0 CB A:THR205 4.9 16.9 1.0 O A:HOH545 5.0 29.8 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