Magnesium in PDB 5lkk: Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 3- Fucosyllactose (3FL)

The structure of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 3- Fucosyllactose (3FL), PDB code: 5lkk 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)	48.90 / 1.49
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.140, 86.710, 96.170, 90.00, 90.00, 90.00
R / Rfree (%)	13.1 / 16.4

The binding sites of Magnesium atom in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 3- Fucosyllactose (3FL) (pdb code 5lkk). 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 3- Fucosyllactose (3FL), PDB code: 5lkk:
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 3- Fucosyllactose (3FL)


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 3- Fucosyllactose (3FL) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg605 b:17.6 occ:1.00 H A:PHE517 2.4 22.9 1.0 HE A:ARG516 2.4 38.3 1.0 H A:LEU229 2.4 19.7 1.0 HB3 A:PHE517 3.1 23.6 1.0 O A:HOH952 3.1 40.8 1.0 O A:HOH817 3.1 40.0 1.0 HA A:ARG516 3.2 22.4 1.0 N A:PHE517 3.2 19.1 1.0 HA A:SER228 3.2 21.5 1.0 NE A:ARG516 3.2 31.9 1.0 N A:LEU229 3.2 16.4 1.0 HH21 A:ARG516 3.3 44.2 1.0 HB2 A:LEU229 3.3 19.1 1.0 HB2 A:SER228 3.5 21.6 1.0 HB2 A:PHE517 3.7 23.6 1.0 HG A:LEU229 3.7 19.6 1.0 CB A:PHE517 3.7 19.7 1.0 HD11 A:ILE231 3.8 31.2 1.0 HD2 A:ARG516 3.8 33.9 1.0 O A:LEU229 3.8 17.6 1.0 HB3 A:ARG516 3.9 24.3 1.0 CA A:SER228 3.9 17.9 1.0 CA A:ARG516 3.9 18.7 1.0 NH2 A:ARG516 3.9 36.9 1.0 CB A:LEU229 4.0 15.9 1.0 CZ A:ARG516 4.0 35.5 1.0 CA A:PHE517 4.1 18.9 1.0 C A:ARG516 4.1 18.7 1.0 C A:SER228 4.1 16.5 1.0 CA A:LEU229 4.1 15.3 1.0 CD A:ARG516 4.1 28.3 1.0 HD12 A:LEU229 4.1 20.0 1.0 CB A:SER228 4.1 18.0 1.0 CG A:LEU229 4.3 16.3 1.0 CB A:ARG516 4.4 20.2 1.0 HD13 A:ILE231 4.4 31.2 1.0 C A:LEU229 4.4 15.7 1.0 CD1 A:ILE231 4.5 26.0 1.0 HB3 A:SER228 4.5 21.6 1.0 O A:PHE517 4.6 21.2 1.0 O A:HOH751 4.7 30.6 1.0 CD1 A:LEU229 4.7 16.6 1.0 HH22 A:ARG516 4.7 44.2 1.0 HA A:PHE517 4.8 22.6 1.0 HD3 A:ARG516 4.9 33.9 1.0 HB3 A:LEU229 4.9 19.1 1.0 CG A:ARG516 4.9 23.7 1.0 C A:PHE517 4.9 20.3 1.0 HD12 A:ILE231 4.9 31.2 1.0 HD2 A:PHE517 4.9 28.1 1.0 HA A:LEU229 5.0 18.4 1.0

Magnesium binding site 2 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with 3- Fucosyllactose (3FL)


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 3- Fucosyllactose (3FL) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg604 b:22.6 occ:1.00 H B:LEU229 2.3 23.9 1.0 H B:PHE517 2.4 28.3 1.0 HE B:ARG516 2.4 44.3 1.0 HB3 B:PHE517 3.1 30.6 1.0 HA B:ARG516 3.2 27.8 1.0 N B:LEU229 3.2 19.9 1.0 N B:PHE517 3.2 23.6 1.0 NE B:ARG516 3.2 36.9 1.0 HA B:SER228 3.2 26.0 1.0 HH21 B:ARG516 3.3 49.5 1.0 HB2 B:LEU229 3.4 22.8 1.0 HB2 B:SER228 3.4 25.9 1.0 HG B:LEU229 3.6 23.3 1.0 HB3 B:ARG516 3.7 32.1 1.0 O B:LEU229 3.8 21.1 1.0 HD2 B:ARG516 3.8 40.3 1.0 CB B:PHE517 3.8 25.6 1.0 HB2 B:PHE517 3.8 30.6 1.0 HD11 B:ILE231 3.9 34.0 1.0 CA B:SER228 3.9 21.6 1.0 CA B:ARG516 3.9 23.1 1.0 CB B:LEU229 4.0 19.0 1.0 NH2 B:ARG516 4.0 41.3 1.0 CA B:LEU229 4.0 18.4 1.0 C B:SER228 4.1 20.5 1.0 CD B:ARG516 4.1 33.6 1.0 C B:ARG516 4.1 23.8 1.0 CZ B:ARG516 4.1 39.8 1.0 CA B:PHE517 4.1 25.0 1.0 CB B:SER228 4.1 21.6 1.0 HD12 B:LEU229 4.2 24.2 1.0 CG B:LEU229 4.2 19.4 1.0 CB B:ARG516 4.3 26.8 1.0 C B:LEU229 4.4 19.2 1.0 HB3 B:SER228 4.5 25.9 1.0 HD13 B:ILE231 4.5 34.0 1.0 O B:PHE517 4.5 28.5 1.0 CD1 B:ILE231 4.6 28.3 1.0 O B:HOH748 4.6 34.1 1.0 CD1 B:LEU229 4.8 20.2 1.0 CG B:ARG516 4.8 29.8 1.0 HH22 B:ARG516 4.8 49.5 1.0 C B:PHE517 4.8 27.8 1.0 HD3 B:ARG516 4.9 40.3 1.0 HD2 B:PHE517 4.9 32.8 1.0 HA B:PHE517 4.9 30.0 1.0 HB3 B:LEU229 4.9 22.8 1.0 HA B:LEU229 4.9 22.1 1.0 HD12 B:ILE231 4.9 34.0 1.0

B.K.Singh, V.Morozov, G.S.Hansman. Structural Basis of Hmos Interaction with the Emerging Gii.17 Norovirus KAWASAKI308 To Be Published.