Potassium in PDB 4x17: Jc Mad-1 Polyomavirus VP1 in Complex with GD1B Oligosaccharide

The structure of Jc Mad-1 Polyomavirus VP1 in Complex with GD1B Oligosaccharide, PDB code: 4x17 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 / 1.75
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	149.740, 95.390, 128.880, 90.00, 110.40, 90.00
R / Rfree (%)	16 / 18.1

The binding sites of Potassium atom in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1B Oligosaccharide (pdb code 4x17). This binding sites where shown within 5.0 Angstroms radius around Potassium atom.
In total 2 binding sites of Potassium where determined in the Jc Mad-1 Polyomavirus VP1 in Complex with GD1B Oligosaccharide, PDB code: 4x17:
Jump to Potassium binding site number: 1; 2;

Potassium binding site 1 out of 2 in the Jc Mad-1 Polyomavirus 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 Mad-1 Polyomavirus VP1 in Complex with GD1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ A:K306 b:20.5 occ:0.50 O A:HOH603 2.3 35.2 1.0 O E:HOH410 2.3 42.6 1.0 O A:HOH474 2.4 43.6 1.0 O A:HOH544 2.5 21.7 1.0 OE2 E:GLU40 2.6 29.9 1.0 O A:THR205 2.6 17.6 1.0 OE1 E:GLU40 3.0 31.2 1.0 CD E:GLU40 3.2 28.3 1.0 C A:THR205 3.5 16.6 1.0 CA A:THR205 4.2 16.4 1.0 N A:ARG206 4.4 16.1 1.0 NZ E:LYS279 4.4 26.4 1.0 OH E:TYR277 4.5 16.6 1.0 CA A:ARG206 4.6 16.3 1.0 CG E:GLU40 4.7 24.8 1.0 OE1 E:GLU38 4.7 27.0 0.5 O A:PRO204 4.8 15.3 1.0 O A:ARG206 4.8 14.5 1.0 CE E:LYS279 4.8 24.1 1.0 CB A:THR205 5.0 16.9 1.0 O A:HOH563 5.0 26.1 1.0

Potassium binding site 2 out of 2 in the Jc Mad-1 Polyomavirus 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 Mad-1 Polyomavirus VP1 in Complex with GD1B Oligosaccharide within 5.0Å range: probe atom residue distance (Å) B Occ D:K307 b:22.2 occ:0.50 O D:HOH501 2.2 41.2 1.0 O E:HOH594 2.3 37.6 1.0 O E:HOH498 2.5 25.4 1.0 O E:THR205 2.6 16.2 1.0 OE2 D:GLU40 2.7 27.0 1.0 OE1 D:GLU40 2.9 28.4 1.0 CD D:GLU40 3.2 26.1 1.0 C E:THR205 3.5 15.1 1.0 CA E:THR205 4.1 15.1 1.0 N E:ARG206 4.4 14.5 1.0 NZ D:LYS279 4.5 23.2 1.0 CA E:ARG206 4.6 14.5 1.0 O D:HOH417 4.7 41.4 1.0 CG D:GLU40 4.7 23.5 1.0 OH D:TYR277 4.7 16.1 1.0 OE2 D:GLU38 4.7 32.1 1.0 O E:PRO204 4.7 13.9 1.0 O E:ARG206 4.8 12.9 1.0 CB E:THR205 4.9 16.1 1.0 CD D:LYS279 5.0 20.5 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