Magnesium in PDB 6xw6: Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853

The structure of Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853, PDB code: 6xw6 was solved by T.Kilic, C.Sabin, G.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.58 / 1.96
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	72.690, 85.290, 77.970, 90.00, 113.47, 90.00
R / Rfree (%)	19.9 / 24.8

The binding sites of Magnesium atom in the Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853 (pdb code 6xw6). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 3 binding sites of Magnesium where determined in the Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853, PDB code: 6xw6:
Jump to Magnesium binding site number: 1; 2; 3;

Magnesium binding site 1 out of 3 in the Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:22.5 occ:1.00 O A:HOH728 1.9 27.5 1.0 OE1 A:GLN438 1.9 22.5 1.0 OD2 A:ASP440 2.0 29.6 1.0 O A:HOH708 2.0 22.7 1.0 O A:HOH802 2.1 28.9 1.0 O A:HOH826 2.2 25.8 1.0 CD A:GLN438 3.0 22.0 1.0 CG A:ASP440 3.1 30.9 1.0 NE2 A:GLN438 3.4 20.4 1.0 CB A:ASP440 3.7 24.9 1.0 O A:ALA445 3.9 26.0 1.0 OE2 A:GLU447 4.0 27.0 1.0 OD1 A:ASP440 4.2 34.9 1.0 O A:HOH818 4.2 27.1 1.0 O A:ASP443 4.2 28.7 1.0 CG A:GLN438 4.3 21.8 1.0 O C:HOH233 4.3 38.2 1.0 O A:HOH866 4.3 30.1 1.0 OD2 A:ASP443 4.4 37.3 1.0 CB A:ASP443 4.4 32.9 1.0 CG A:ASP443 4.6 34.6 1.0 CD A:GLU447 4.9 24.6 1.0 O A:HOH795 4.9 26.3 1.0 C A:ASP443 4.9 31.9 1.0

Magnesium binding site 2 out of 3 in the Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853 within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:41.1 occ:1.00 OD2 A:ASP366 2.1 37.3 1.0 O A:HOH860 2.2 38.1 1.0 O A:HOH807 2.2 24.2 1.0 OD1 A:ASP410 2.2 35.7 1.0 O A:HOH709 2.3 41.7 1.0 O A:HOH852 2.4 40.7 1.0 CG A:ASP410 3.2 36.5 1.0 CG A:ASP366 3.3 35.3 1.0 OD2 A:ASP410 3.6 39.1 1.0 CA A:ASP366 3.8 30.4 1.0 CB A:ASP366 4.0 34.0 1.0 N A:ASP366 4.1 27.1 1.0 O A:ASP410 4.2 27.4 1.0 OD1 A:ASP366 4.3 38.3 1.0 O A:THR363 4.4 23.6 1.0 CB A:ASP410 4.5 30.0 1.0 C A:ASP410 4.6 27.4 1.0 OE2 A:GLU407 4.6 31.9 1.0 CA A:ASP410 4.7 28.3 1.0 OE1 A:GLU407 5.0 29.3 1.0 CD A:GLU407 5.0 26.7 1.0

Magnesium binding site 3 out of 3 in the Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Crystal Structure of Murine Norovirus P Domain in Complex with Nanobody Nb-5853 within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:29.8 occ:1.00 OE1 B:GLN438 1.9 25.1 1.0 O B:HOH777 1.9 34.5 1.0 O B:HOH835 2.2 24.3 1.0 O B:HOH816 2.2 29.4 1.0 O B:HOH722 2.3 33.3 1.0 OD2 B:ASP440 2.3 32.5 1.0 CD B:GLN438 2.9 23.6 1.0 CG B:ASP440 3.3 37.2 1.0 NE2 B:GLN438 3.4 22.1 1.0 CB B:ASP440 3.7 32.9 1.0 OE2 B:GLU447 3.9 30.9 1.0 O B:ALA445 4.0 30.0 1.0 O B:HOH789 4.0 22.7 1.0 CG B:GLN438 4.2 24.7 1.0 O B:ASP443 4.3 34.5 1.0 OD1 B:ASP440 4.4 41.5 1.0 CB B:ASP443 4.5 38.7 1.0 OD2 B:ASP443 4.5 46.1 1.0 O B:HOH775 4.7 24.6 1.0 CG B:ASP443 4.8 39.2 1.0 CD B:GLU447 4.9 27.9 1.0

A.D.Koromyslova, J.M.Devant, T.Kilic, C.D.Sabin, V.Malak, G.Hofhaus, G.S.Hansman. Nanobody Mediated Neutralization Reveals An Achilles Heel For Norovirus To Be Published.