Magnesium in PDB 7vs8: Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.

The structure of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen., PDB code: 7vs8 was solved by K.Murayama, M.Kato-Murayama, M.Shirouzu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	41.19 / 2.40
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	183.749, 76.464, 103.281, 90, 124.2, 90
R / Rfree (%)	16.5 / 19.6

The structure of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. also contains other interesting chemical elements:

Chlorine

(Cl)

11 atoms

The binding sites of Magnesium atom in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. (pdb code 7vs8). 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 P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen., PDB code: 7vs8:
Jump to Magnesium binding site number: 1; 2;

Magnesium binding site 1 out of 2 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


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 P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:42.4 occ:1.00 O A:HOH803 2.1 41.2 1.0 O A:HOH727 2.1 35.0 1.0 O A:HOH841 2.3 41.5 1.0 O A:HOH846 2.3 38.5 1.0 O A:HOH871 2.3 41.1 1.0 OG A:SER322 2.3 38.4 1.0 CB A:SER322 3.3 36.0 1.0 O A:GLU321 3.9 38.2 1.0 O A:GLY281 4.0 35.8 1.0 CA A:SER322 4.0 38.5 1.0 O A:HOH714 4.1 37.3 1.0 O A:HOH798 4.1 31.0 1.0 O A:HOH804 4.2 35.5 1.0 OE2 A:GLU321 4.2 51.9 1.0 O A:HOH867 4.2 42.9 1.0 OE1 A:GLU321 4.4 58.8 1.0 CD A:GLU321 4.6 54.9 1.0 C A:GLU321 4.7 41.7 1.0 N A:SER322 4.7 40.0 1.0 O A:HOH887 4.7 41.9 1.0 CD A:PRO323 4.8 34.6 1.0

Magnesium binding site 2 out of 2 in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen.


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 P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis B Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:43.2 occ:1.00 O B:HOH805 2.1 39.9 1.0 O B:HOH872 2.2 43.0 1.0 O B:HOH854 2.2 41.8 1.0 O B:HOH731 2.2 33.6 1.0 OG B:SER322 2.3 39.9 1.0 O B:HOH853 2.4 37.9 1.0 CB B:SER322 3.3 36.6 1.0 O B:HOH796 4.1 29.3 1.0 O B:GLU321 4.1 37.1 1.0 O B:HOH788 4.1 32.6 1.0 O B:GLY281 4.1 35.3 1.0 CA B:SER322 4.1 39.9 1.0 OE2 B:GLU321 4.1 50.0 1.0 O B:HOH863 4.3 45.0 1.0 OE1 B:GLU321 4.3 58.5 1.0 O B:HOH707 4.4 38.0 1.0 O B:HOH886 4.5 43.9 1.0 CD B:GLU321 4.5 53.3 1.0 C B:GLU321 4.8 40.3 1.0 N B:SER322 4.8 40.0 1.0 O B:HOH871 5.0 44.4 1.0

T.Kimura-Someya, M.Kato-Murayama, K.Katsura, N.Sakai, K.Murayama, K.Hanada, M.Shirouzu, Y.Someya. Lewis Fucose Is A Key Moiety For the Recognition of Histo-Blood Group Antigens By Gi.9 Norovirus, As Revealed By Structural Analysis. Febs Open Bio V. 12 560 2022.
ISSN: ESSN 2211-5463
PubMed: 35038379
DOI: 10.1002/2211-5463.13370