Magnesium in PDB 5lkc: Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with Hbga Type A (Triglycan)

The structure of Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with Hbga Type A (Triglycan), PDB code: 5lkc 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)	48.72 / 1.81
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.870, 86.730, 97.440, 90.00, 90.00, 90.00
R / Rfree (%)	15.3 / 18.3

The binding sites of Magnesium atom in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with Hbga Type A (Triglycan) (pdb code 5lkc). 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 Hbga Type A (Triglycan), PDB code: 5lkc:
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 Hbga Type A (Triglycan)


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 Hbga Type A (Triglycan) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg603 b:14.7 occ:1.00 H A:PHE517 2.3 23.5 1.0 H A:LEU229 2.4 19.9 1.0 HE A:ARG516 2.5 50.1 1.0 HB3 A:PHE517 3.1 23.5 1.0 N A:PHE517 3.2 19.6 1.0 HA A:ARG516 3.2 24.0 1.0 N A:LEU229 3.2 16.6 1.0 HA A:SER228 3.3 23.1 1.0 O A:HOH906 3.3 39.6 1.0 NE A:ARG516 3.3 41.8 1.0 HH21 A:ARG516 3.3 63.9 1.0 HB2 A:LEU229 3.4 20.5 1.0 HB2 A:SER228 3.6 26.5 1.0 HG A:LEU229 3.7 21.6 1.0 HB2 A:PHE517 3.7 23.5 1.0 CB A:PHE517 3.7 19.6 1.0 O A:LEU229 3.8 20.3 1.0 HB3 A:ARG516 3.8 28.1 1.0 HD2 A:ARG516 3.9 40.9 1.0 HD11 A:ILE231 3.9 55.0 1.0 CA A:ARG516 4.0 20.0 1.0 CA A:SER228 4.0 19.3 1.0 NH2 A:ARG516 4.0 53.2 1.0 CB A:LEU229 4.0 17.1 1.0 CA A:PHE517 4.0 19.4 1.0 C A:ARG516 4.1 20.5 1.0 CA A:LEU229 4.1 16.1 1.0 C A:SER228 4.1 18.1 1.0 CZ A:ARG516 4.1 50.0 1.0 CD A:ARG516 4.2 34.1 1.0 CB A:SER228 4.2 22.1 1.0 HD12 A:LEU229 4.2 22.5 1.0 CG A:LEU229 4.3 18.0 1.0 CB A:ARG516 4.4 23.4 1.0 C A:LEU229 4.4 17.8 1.0 HD13 A:ILE231 4.4 55.0 1.0 O A:HOH725 4.6 42.6 1.0 CD1 A:ILE231 4.6 45.9 1.0 O A:PHE517 4.6 20.5 1.0 HB3 A:SER228 4.6 26.5 1.0 HA A:PHE517 4.8 23.3 1.0 CD1 A:LEU229 4.8 18.7 1.0 O A:HOH811 4.8 41.4 1.0 HH22 A:ARG516 4.8 63.9 1.0 C A:PHE517 4.9 20.2 1.0 HB3 A:LEU229 4.9 20.5 1.0 CG A:ARG516 4.9 28.1 1.0 HD12 A:ILE231 4.9 55.0 1.0 HD3 A:ARG516 4.9 40.9 1.0 HD2 A:PHE517 5.0 31.3 1.0 HA A:LEU229 5.0 19.3 1.0

Magnesium binding site 2 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 in Complex with Hbga Type A (Triglycan)


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 Hbga Type A (Triglycan) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg603 b:18.1 occ:1.00 H B:LEU229 2.3 23.4 1.0 H B:PHE517 2.4 27.1 1.0 HE B:ARG516 2.4 54.8 1.0 HB3 B:PHE517 3.1 29.7 1.0 N B:LEU229 3.2 19.5 1.0 N B:PHE517 3.2 22.6 1.0 HA B:ARG516 3.2 30.3 1.0 HA B:SER228 3.3 24.7 1.0 NE B:ARG516 3.3 45.7 1.0 HH21 B:ARG516 3.3 59.7 1.0 HB2 B:SER228 3.4 28.8 1.0 HB2 B:LEU229 3.4 20.9 1.0 HG B:LEU229 3.7 22.9 1.0 CB B:PHE517 3.8 24.8 1.0 HB3 B:ARG516 3.8 36.5 1.0 O B:LEU229 3.8 21.0 1.0 HB2 B:PHE517 3.8 29.7 1.0 HD2 B:ARG516 3.8 49.2 1.0 HD11 B:ILE231 3.9 50.3 1.0 CA B:SER228 3.9 20.6 1.0 CA B:ARG516 4.0 25.2 1.0 NH2 B:ARG516 4.0 49.7 1.0 CB B:LEU229 4.0 17.5 1.0 CA B:LEU229 4.0 18.0 1.0 CA B:PHE517 4.0 23.9 1.0 C B:SER228 4.1 18.9 1.0 C B:ARG516 4.1 23.9 1.0 CZ B:ARG516 4.1 46.9 1.0 CB B:SER228 4.1 24.0 1.0 CD B:ARG516 4.1 41.0 1.0 CG B:LEU229 4.3 19.1 1.0 CB B:ARG516 4.3 30.4 1.0 HD12 B:LEU229 4.3 25.8 1.0 C B:LEU229 4.4 18.4 1.0 HD13 B:ILE231 4.4 50.3 1.0 HB3 B:SER228 4.5 28.8 1.0 O B:PHE517 4.5 26.2 1.0 CD1 B:ILE231 4.6 41.9 1.0 O B:HOH712 4.6 29.4 1.0 HH22 B:ARG516 4.8 59.7 1.0 C B:PHE517 4.8 25.1 1.0 HA B:PHE517 4.8 28.6 1.0 HD12 B:ILE231 4.9 50.3 1.0 CG B:ARG516 4.9 35.6 1.0 CD1 B:LEU229 4.9 21.5 1.0 HD3 B:ARG516 4.9 49.2 1.0 HD2 B:PHE517 4.9 33.1 1.0 HA B:LEU229 4.9 21.6 1.0 HB3 B:LEU229 4.9 20.9 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