Magnesium in PDB 5f4o: Protruding Domain of Gii.17 Norovirus KAWASAKI308

The structure of Protruding Domain of Gii.17 Norovirus KAWASAKI308, PDB code: 5f4o was solved by B.K.Singh, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	43.49 / 1.59
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	75.720, 86.970, 97.350, 90.00, 90.00, 90.00
R / Rfree (%)	15.1 / 17.4

The binding sites of Magnesium atom in the Protruding Domain of Gii.17 Norovirus KAWASAKI308 (pdb code 5f4o). 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, PDB code: 5f4o:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308


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 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg606 b:22.4 occ:1.00 H A:LEU229 2.4 25.7 1.0 HE A:ARG516 2.4 45.9 1.0 H A:PHE517 2.4 27.3 1.0 HB3 A:PHE517 3.1 27.6 1.0 HH21 A:ARG516 3.1 59.4 1.0 N A:LEU229 3.2 21.4 1.0 NE A:ARG516 3.2 38.2 1.0 N A:PHE517 3.3 22.7 1.0 HA A:ARG516 3.3 27.8 1.0 HA A:SER228 3.3 25.2 1.0 HB2 A:LEU229 3.4 20.2 1.0 HB2 A:SER228 3.5 23.5 1.0 HG A:LEU229 3.6 22.9 1.0 O A:LEU229 3.8 20.3 1.0 HB3 A:ARG516 3.8 33.2 1.0 CB A:PHE517 3.8 23.0 1.0 NH2 A:ARG516 3.8 49.5 1.0 HB2 A:PHE517 3.9 27.6 1.0 HD2 A:ARG516 3.9 47.9 1.0 CA A:SER228 3.9 21.0 1.0 HD11 A:ILE231 4.0 41.0 1.0 CA A:ARG516 4.0 23.1 1.0 CB A:LEU229 4.0 16.9 1.0 CZ A:ARG516 4.0 41.2 1.0 CA A:LEU229 4.0 18.2 1.0 C A:SER228 4.1 20.6 1.0 CA A:PHE517 4.1 22.0 1.0 C A:ARG516 4.1 24.1 1.0 CB A:SER228 4.1 19.6 1.0 CD A:ARG516 4.1 40.0 1.0 HD12 A:LEU229 4.2 25.0 1.0 CG A:LEU229 4.2 19.1 1.0 CB A:ARG516 4.3 27.6 1.0 C A:LEU229 4.4 18.5 1.0 HB3 A:SER228 4.5 23.5 1.0 HD13 A:ILE231 4.5 41.0 1.0 O A:PHE517 4.6 28.2 1.0 HH22 A:ARG516 4.6 59.4 1.0 CD1 A:ILE231 4.7 34.1 1.0 O A:HOH747 4.7 30.3 1.0 CD1 A:LEU229 4.8 20.9 1.0 C A:PHE517 4.9 25.1 1.0 CG A:ARG516 4.9 26.4 1.0 HB3 A:LEU229 4.9 20.2 1.0 HA A:PHE517 4.9 26.4 1.0 HD2 A:PHE517 4.9 32.0 1.0 HA A:LEU229 4.9 21.9 1.0 HD3 A:ARG516 4.9 47.9 1.0

Magnesium binding site 2 out of 2 in the Protruding Domain of Gii.17 Norovirus KAWASAKI308


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 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg605 b:20.6 occ:1.00 H B:PHE517 2.4 23.2 1.0 HE B:ARG516 2.4 41.5 1.0 H B:LEU229 2.4 21.4 1.0 O B:HOH757 3.0 36.6 1.0 HB3 B:PHE517 3.1 23.8 1.0 HA B:SER228 3.2 20.4 1.0 N B:PHE517 3.2 19.3 1.0 HA B:ARG516 3.3 23.0 1.0 NE B:ARG516 3.3 34.6 1.0 N B:LEU229 3.3 17.9 1.0 HH21 B:ARG516 3.3 49.2 1.0 HB2 B:LEU229 3.4 17.9 1.0 HB2 B:SER228 3.5 24.6 1.0 HG B:LEU229 3.7 16.9 1.0 CB B:PHE517 3.8 19.8 1.0 HB2 B:PHE517 3.8 23.8 1.0 HD2 B:ARG516 3.8 33.6 1.0 HD11 B:ILE231 3.8 40.0 1.0 O B:LEU229 3.8 16.5 1.0 HB3 B:ARG516 3.9 24.4 1.0 CA B:SER228 3.9 17.0 1.0 NH2 B:ARG516 4.0 41.0 1.0 CA B:ARG516 4.0 19.2 1.0 CB B:LEU229 4.0 14.9 1.0 CZ B:ARG516 4.1 40.2 1.0 CA B:PHE517 4.1 19.5 1.0 CA B:LEU229 4.1 14.8 1.0 C B:SER228 4.1 16.6 1.0 C B:ARG516 4.1 20.0 1.0 CD B:ARG516 4.1 28.0 1.0 CB B:SER228 4.2 20.5 1.0 HD12 B:LEU229 4.2 19.4 1.0 CG B:LEU229 4.3 14.0 1.0 CB B:ARG516 4.4 20.3 1.0 HD13 B:ILE231 4.4 40.0 1.0 C B:LEU229 4.4 17.1 1.0 HB3 B:SER228 4.5 24.6 1.0 CD1 B:ILE231 4.5 33.3 1.0 O B:PHE517 4.7 21.2 1.0 O B:HOH765 4.7 29.7 1.0 HH22 B:ARG516 4.8 49.2 1.0 CD1 B:LEU229 4.8 16.2 1.0 HA B:PHE517 4.8 23.4 1.0 HD3 B:ARG516 4.9 33.6 1.0 HD2 B:PHE517 4.9 29.9 1.0 CG B:ARG516 4.9 20.8 1.0 C B:PHE517 4.9 21.9 1.0 HD12 B:ILE231 4.9 40.0 1.0 HB3 B:LEU229 4.9 17.9 1.0 HA B:LEU229 5.0 17.7 1.0

B.K.Singh, A.Koromyslova, L.Hefele, C.Gurth, G.S.Hansman. Structural Evolution of the Emerging 2014-2015 Gii.17 Noroviruses. J.Virol. V. 90 2710 2015.
ISSN: ESSN 1098-5514
PubMed: 26699640
DOI: 10.1128/JVI.03119-15