Magnesium in PDB 5lkg: Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl)

The structure of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl), PDB code: 5lkg was solved by B.K.Singh, V.Morozov, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.30 / 1.51
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	76.200, 86.680, 97.060, 90.00, 90.00, 90.00
R / Rfree (%)	16.3 / 20.4

The binding sites of Magnesium atom in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl) (pdb code 5lkg). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl), PDB code: 5lkg:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg604 b:20.6 occ:1.00 H A:LEU229 2.3 23.8 1.0 H A:PHE517 2.3 25.9 1.0 HE A:ARG516 2.5 38.9 1.0 HB3 A:PHE517 3.0 28.5 1.0 HA A:SER228 3.1 23.9 1.0 N A:LEU229 3.1 19.8 1.0 N A:PHE517 3.2 21.6 1.0 HA A:ARG516 3.2 25.0 1.0 HH21 A:ARG516 3.2 43.1 1.0 NE A:ARG516 3.3 32.4 1.0 HB2 A:SER228 3.4 25.1 1.0 HB2 A:LEU229 3.4 21.3 1.0 HB3 A:ARG516 3.6 29.0 1.0 HG A:LEU229 3.6 23.4 1.0 CB A:PHE517 3.7 23.8 1.0 HB2 A:PHE517 3.8 28.5 1.0 O A:LEU229 3.8 20.6 1.0 CA A:SER228 3.8 19.9 1.0 HD11 A:ILE231 3.9 32.9 1.0 CA A:ARG516 3.9 20.9 1.0 NH2 A:ARG516 3.9 35.9 1.0 CB A:LEU229 4.0 17.8 1.0 HD2 A:ARG516 4.0 35.8 1.0 C A:SER228 4.0 19.0 1.0 CA A:LEU229 4.0 19.2 1.0 CB A:SER228 4.0 20.9 1.0 CA A:PHE517 4.0 22.4 1.0 C A:ARG516 4.1 21.7 1.0 CZ A:ARG516 4.1 33.5 1.0 CB A:ARG516 4.2 24.2 1.0 CD A:ARG516 4.2 29.8 1.0 CG A:LEU229 4.2 19.5 1.0 HD12 A:LEU229 4.3 23.4 1.0 C A:LEU229 4.4 18.6 1.0 HB3 A:SER228 4.4 25.1 1.0 O A:PHE517 4.5 25.9 1.0 HD13 A:ILE231 4.5 32.9 1.0 CD1 A:ILE231 4.6 27.4 1.0 O A:HOH733 4.7 32.0 1.0 HH22 A:ARG516 4.7 43.1 1.0 C A:PHE517 4.8 23.6 1.0 CD1 A:LEU229 4.8 19.5 1.0 HA A:PHE517 4.8 26.9 1.0 CG A:ARG516 4.8 27.8 1.0 HB3 A:LEU229 4.9 21.3 1.0 HD2 A:PHE517 4.9 30.8 1.0 HA A:LEU229 4.9 23.1 1.0 HB2 A:ARG516 5.0 29.0 1.0

Magnesium binding site 2 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 2- Fucosyllactose (2'Fl) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:18.6 occ:1.00 H B:LEU229 2.4 23.4 1.0 HE B:ARG516 2.4 43.9 1.0 H B:PHE517 2.4 26.0 1.0 HB3 B:PHE517 3.1 26.9 1.0 O B:HOH927 3.1 45.5 1.0 HA B:ARG516 3.2 27.1 1.0 N B:LEU229 3.2 19.5 1.0 NE B:ARG516 3.2 36.6 1.0 N B:PHE517 3.3 21.6 1.0 HA B:SER228 3.3 23.8 1.0 HH21 B:ARG516 3.3 49.1 1.0 HB2 B:LEU229 3.3 21.3 1.0 HB2 B:SER228 3.5 24.9 1.0 HG B:LEU229 3.7 23.3 1.0 HB2 B:PHE517 3.7 26.9 1.0 CB B:PHE517 3.8 22.4 1.0 O B:LEU229 3.8 20.5 1.0 HD2 B:ARG516 3.8 40.2 1.0 HB3 B:ARG516 3.8 30.3 1.0 HD11 B:ILE231 3.9 36.1 1.0 CA B:SER228 3.9 19.8 1.0 NH2 B:ARG516 3.9 41.0 1.0 CA B:ARG516 4.0 22.6 1.0 CB B:LEU229 4.0 17.7 1.0 CA B:LEU229 4.1 18.7 1.0 CZ B:ARG516 4.1 39.8 1.0 C B:SER228 4.1 18.8 1.0 CD B:ARG516 4.1 33.5 1.0 CA B:PHE517 4.1 22.5 1.0 C B:ARG516 4.1 22.6 1.0 CB B:SER228 4.1 20.8 1.0 HD12 B:LEU229 4.2 25.0 1.0 CG B:LEU229 4.3 19.4 1.0 CB B:ARG516 4.3 25.2 1.0 HD13 B:ILE231 4.4 36.1 1.0 C B:LEU229 4.4 18.7 1.0 HB3 B:SER228 4.5 24.9 1.0 CD1 B:ILE231 4.6 30.1 1.0 O B:HOH726 4.6 33.8 1.0 O B:PHE517 4.7 22.9 1.0 HH22 B:ARG516 4.7 49.1 1.0 O B:HOH729 4.8 34.6 1.0 CD1 B:LEU229 4.8 20.8 1.0 HD12 B:ILE231 4.8 36.1 1.0 HB3 B:LEU229 4.8 21.3 1.0 HA B:PHE517 4.8 26.9 1.0 CG B:ARG516 4.9 29.2 1.0 HD3 B:ARG516 4.9 40.2 1.0 HD2 B:PHE517 4.9 30.4 1.0 HA B:LEU229 4.9 22.5 1.0 C B:PHE517 4.9 22.4 1.0 O B:PHE515 5.0 21.0 1.0

A.Koromyslova, S.Tripathi, V.Morozov, H.Schroten, G.S.Hansman. Human Norovirus Inhibition By A Human Milk Oligosaccharide. Virology V. 508 81 2017.
ISSN: ISSN 1096-0341
PubMed: 28505592
DOI: 10.1016/J.VIROL.2017.04.032