Magnesium in PDB 7vs9: Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X Antigen.

The structure of Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X Antigen., PDB code: 7vs9 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)	35.21 / 2.26
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	184.2, 77.244, 103.526, 90, 124.2, 90
R / Rfree (%)	16.5 / 19.5

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

Chlorine

(Cl)

16 atoms

The binding sites of Magnesium atom in the Crystal Structure of P Domain From Norovirus Gi.9 Capsid Protein in Complex with Lewis X Antigen. (pdb code 7vs9). 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 X Antigen., PDB code: 7vs9:
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 X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg601 b:39.3 occ:1.00 O A:HOH779 2.1 34.7 1.0 O A:HOH879 2.1 39.7 1.0 O A:HOH928 2.2 36.6 1.0 O A:HOH833 2.2 34.6 1.0 OG A:SER322 2.3 37.9 1.0 O A:HOH717 2.3 34.1 1.0 CB A:SER322 3.4 36.4 1.0 O A:GLU321 4.1 37.5 1.0 OE1 A:GLU321 4.1 55.0 1.0 CA A:SER322 4.1 37.6 1.0 O A:GLY281 4.2 28.2 1.0 O A:HOH912 4.2 44.0 1.0 OE2 A:GLU321 4.2 51.6 1.0 O A:HOH728 4.3 36.3 1.0 O A:HOH814 4.3 33.7 1.0 O A:HOH924 4.3 45.5 1.0 CD A:GLU321 4.5 49.1 1.0 C A:GLU321 4.8 40.0 1.0 N A:SER322 4.8 41.1 1.0 O A:HOH961 4.8 41.5 1.0 O A:HOH923 5.0 41.1 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 X 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 X Antigen. within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg601 b:43.1 occ:1.00 O B:HOH805 2.1 36.7 1.0 O B:HOH862 2.2 39.6 1.0 O B:HOH923 2.2 36.5 1.0 O B:HOH819 2.2 33.5 1.0 O B:HOH727 2.3 33.6 1.0 OG B:SER322 2.4 37.5 1.0 CB B:SER322 3.4 37.8 1.0 O B:GLU321 4.1 37.2 1.0 O B:GLY281 4.2 29.8 1.0 OE1 B:GLU321 4.2 57.6 1.0 CA B:SER322 4.2 36.8 1.0 OE2 B:GLU321 4.3 50.3 1.0 O B:HOH803 4.3 33.3 1.0 O B:HOH731 4.3 35.7 1.0 O B:HOH917 4.3 43.8 1.0 CD B:GLU321 4.5 50.0 1.0 O B:HOH958 4.7 44.1 1.0 C B:GLU321 4.8 39.3 1.0 N B:SER322 4.8 39.1 1.0 O B:HOH926 4.9 41.3 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