Magnesium in PDB 6h9v: Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc

The structure of Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc, PDB code: 6h9v was solved by P.H.O.Meyer, B.S.Blaum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	39.58 / 1.52
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	54.290, 83.950, 65.130, 90.00, 95.78, 90.00
R / Rfree (%)	14.7 / 18.3

The binding sites of Magnesium atom in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc (pdb code 6h9v). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 2 binding sites of Magnesium where determined in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc, PDB code: 6h9v:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc


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 Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg602 b:32.1 occ:1.00 H A:GLU488 2.2 23.6 1.0 HG2 A:GLU488 2.8 29.8 1.0 O A:ALA528 2.8 25.6 1.0 HA A:PHE487 2.8 23.8 1.0 HB2 A:PHE487 2.8 27.3 1.0 HB1 A:ALA528 3.0 37.1 1.0 N A:GLU488 3.0 19.7 1.0 HB3 A:MET530 3.0 44.6 1.0 O A:HOH892 3.1 38.1 1.0 CA A:PHE487 3.4 19.9 1.0 O A:PRO529 3.4 34.3 1.0 CB A:PHE487 3.5 22.8 1.0 O A:HOH832 3.6 18.3 1.0 C A:ALA528 3.6 27.7 1.0 CG A:GLU488 3.6 24.8 1.0 C A:PHE487 3.7 20.7 1.0 HG3 A:GLU488 3.8 29.8 1.0 CB A:ALA528 3.8 30.9 1.0 O A:GLU488 3.8 21.6 1.0 HB3 A:PHE487 3.8 27.3 1.0 C A:PRO529 3.9 29.7 1.0 CB A:MET530 3.9 37.2 1.0 HB2 A:ALA528 4.0 37.1 1.0 HA A:MET530 4.0 40.6 1.0 CA A:GLU488 4.1 18.6 1.0 N A:MET530 4.2 30.5 1.0 CA A:ALA528 4.2 26.7 1.0 CA A:MET530 4.3 33.9 1.0 CB A:GLU488 4.3 25.9 1.0 C A:GLU488 4.4 19.9 1.0 H A:ALA528 4.4 31.3 1.0 HB2 A:MET530 4.5 44.6 1.0 HG2 A:MET530 4.5 45.4 1.0 N A:PRO529 4.5 27.1 1.0 HD1 A:PHE487 4.5 25.9 1.0 HB3 A:GLU488 4.6 31.1 1.0 HB3 A:ALA528 4.6 37.1 1.0 N A:ALA528 4.6 26.1 1.0 H A:MET530 4.6 36.6 1.0 CD A:GLU488 4.7 30.2 1.0 CA A:PRO529 4.7 29.5 1.0 N A:PHE487 4.7 20.7 1.0 HB3 A:LEU527 4.8 27.4 1.0 CG A:PHE487 4.8 20.0 1.0 CG A:MET530 4.8 37.8 1.0 O A:LEU486 4.9 27.4 1.0 HA A:GLU488 4.9 22.3 1.0 O A:PHE487 4.9 20.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc


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 Deaminated P Domain From Norovirus Strain Saga Gii-4 in Complex with Fuc within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg602 b:32.5 occ:1.00 H B:GLU488 2.3 22.2 1.0 O B:ALA528 2.7 25.9 1.0 HG2 B:GLU488 2.7 23.6 1.0 HA B:PHE487 2.8 23.1 1.0 HA B:MET530 2.9 38.1 0.6 O B:HOH790 2.9 33.0 1.0 HB3 B:ALA528 3.0 36.7 1.0 HB2 B:PHE487 3.0 22.6 1.0 N B:GLU488 3.1 18.5 1.0 O B:HOH984 3.2 38.5 1.0 O B:PRO529 3.3 32.8 1.0 HA B:MET530 3.4 43.2 0.4 CA B:PHE487 3.4 19.2 1.0 C B:ALA528 3.6 24.9 1.0 CG B:GLU488 3.6 19.7 1.0 CB B:PHE487 3.6 18.9 1.0 O B:HOH837 3.7 21.2 1.0 CA B:MET530 3.7 31.8 0.6 C B:PRO529 3.7 35.8 1.0 HG3 B:GLU488 3.7 23.6 1.0 C B:PHE487 3.7 19.6 1.0 CB B:ALA528 3.8 30.6 1.0 O B:GLU488 3.9 19.2 1.0 N B:MET530 3.9 31.8 0.6 HB1 B:ALA528 3.9 36.7 1.0 N B:MET530 4.0 32.0 0.4 HB3 B:PHE487 4.0 22.6 1.0 CA B:MET530 4.1 36.0 0.4 CA B:GLU488 4.1 21.0 1.0 CA B:ALA528 4.2 30.7 1.0 C B:MET530 4.3 35.4 0.6 CB B:GLU488 4.4 21.4 1.0 OXT B:MET530 4.4 39.8 0.6 HB2 B:MET530 4.4 40.5 0.4 N B:PRO529 4.4 25.6 1.0 H B:ALA528 4.4 28.6 1.0 C B:GLU488 4.5 19.7 1.0 H B:MET530 4.5 38.5 0.4 H B:MET530 4.6 38.2 0.6 HB2 B:ALA528 4.6 36.7 1.0 N B:ALA528 4.6 23.9 1.0 HB3 B:GLU488 4.6 25.7 1.0 CA B:PRO529 4.6 25.9 1.0 CD B:GLU488 4.7 37.5 1.0 HD1 B:PHE487 4.7 25.6 1.0 HB3 B:LEU527 4.7 27.8 1.0 N B:PHE487 4.8 19.8 1.0 CB B:MET530 4.8 33.8 0.4 O B:LEU486 4.8 22.8 1.0 CB B:MET530 4.8 33.4 0.6 HB2 B:MET530 4.9 40.1 0.6 HG3 B:MET530 4.9 42.9 0.4 HG3 B:MET530 4.9 41.8 0.6 CG B:PHE487 4.9 19.7 1.0 O B:PHE487 4.9 19.3 1.0 HA B:GLU488 4.9 25.1 1.0 OE2 B:GLU488 5.0 30.8 1.0 HA B:PRO529 5.0 31.1 1.0

A.Mallagaray, R.Creutznacher, J.Dulfer, P.H.O.Mayer, L.L.Grimm, J.M.Orduna, E.Trabjerg, T.Stehle, K.D.Rand, B.S.Blaum, C.Uetrecht, T.Peters. A Post-Translational Modification of Human Norovirus Capsid Protein Attenuates Glycan Binding. Nat Commun V. 10 1320 2019.
ISSN: ESSN 2041-1723
PubMed: 30899001
DOI: 10.1038/S41467-019-09251-5