Sodium in PDB 6h6l: Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)

The structure of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca), PDB code: 6h6l was solved by T.Kilic, G.S.Hansman, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.71 / 2.50
Space group	P 41
Cell size a, b, c (Å), α, β, γ (°)	87.000, 87.000, 276.810, 90.00, 90.00, 90.00
R / Rfree (%)	18.9 / 21.6

The structure of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) also contains other interesting chemical elements:

Magnesium

(Mg)

8 atoms

The binding sites of Sodium atom in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) (pdb code 6h6l). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca), PDB code: 6h6l:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na604 b:43.8 occ:1.00 O A:ASN364 2.4 54.5 1.0 O E:LYS94 2.4 47.3 1.0 O E:GLY96 2.4 46.9 1.0 OD1 E:ASP98 2.6 46.4 1.0 OD2 A:ASP366 2.6 58.0 1.0 C A:ASN364 3.4 53.5 1.0 CG E:ASP98 3.5 46.1 1.0 CG A:ASP366 3.5 56.6 1.0 C E:GLY96 3.5 46.7 1.0 C E:LYS94 3.6 48.7 1.0 N E:GLY96 3.7 47.2 1.0 OD1 A:ASP366 3.7 58.2 1.0 OD2 E:ASP98 3.9 45.6 1.0 CA A:ALA365 4.0 51.7 1.0 N A:ALA365 4.1 51.7 1.0 CA E:GLY96 4.1 46.9 1.0 C E:GLY95 4.2 48.3 1.0 N E:LYS94 4.2 47.2 1.0 C A:ALA365 4.3 51.5 1.0 N E:ASP98 4.3 48.0 1.0 CA A:ASN364 4.4 54.7 1.0 CA E:GLY95 4.4 48.6 1.0 N E:GLY95 4.5 49.7 1.0 CA E:LYS94 4.6 49.3 1.0 N A:ASP366 4.6 51.6 1.0 N E:LEU97 4.6 46.4 1.0 CB E:ASP98 4.6 47.1 1.0 CB A:ASN364 4.7 56.5 1.0 O A:ALA365 4.7 51.7 1.0 C E:LEU97 4.7 49.1 1.0 O A:HOH705 4.8 49.8 1.0 CB A:ASP366 4.8 53.9 1.0 CA E:ASP98 4.8 48.0 1.0 CA E:LEU97 4.9 46.9 1.0 CG E:LYS94 5.0 51.0 1.0

Sodium binding site 2 out of 4 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na605 b:33.9 occ:1.00 O F:LYS94 2.3 44.2 1.0 O B:ASN364 2.4 46.5 1.0 O F:HOH507 2.4 57.3 1.0 OD1 F:ASP98 2.4 47.9 1.0 O F:GLY96 2.5 46.7 1.0 CG F:ASP98 3.3 46.9 1.0 OD2 B:ASP366 3.3 67.8 1.0 C B:ASN364 3.5 44.1 1.0 C F:LYS94 3.5 43.8 1.0 C F:GLY96 3.5 45.6 1.0 OD2 F:ASP98 3.6 48.1 1.0 N F:GLY96 3.7 43.3 1.0 CG B:ASP366 4.1 65.2 1.0 N F:LYS94 4.1 43.3 1.0 CA F:GLY96 4.2 43.6 1.0 C F:GLY95 4.2 44.4 1.0 CA B:ALA365 4.2 43.5 1.0 N B:ALA365 4.2 43.6 1.0 N F:ASP98 4.3 42.5 1.0 O B:HOH726 4.3 44.3 1.0 OD1 B:ASP366 4.3 70.0 1.0 CA F:GLY95 4.4 43.2 1.0 N F:GLY95 4.4 43.7 1.0 CA F:LYS94 4.4 44.2 1.0 CB F:ASP98 4.5 44.3 1.0 CA B:ASN364 4.5 44.1 1.0 C B:ALA365 4.5 45.5 1.0 N F:LEU97 4.6 46.1 1.0 CB B:ASN364 4.6 45.6 1.0 C F:LEU97 4.7 43.1 1.0 CA F:ASP98 4.7 42.6 1.0 N B:ASP366 4.9 47.7 1.0 CA F:LEU97 4.9 44.8 1.0 O F:GLY95 5.0 47.0 1.0

Sodium binding site 3 out of 4 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 3 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na604 b:49.8 occ:1.00 O C:ASN364 2.4 61.3 1.0 O G:LYS94 2.4 67.5 1.0 OD1 G:ASP98 2.5 65.7 1.0 O G:GLY96 2.6 64.8 1.0 OD2 C:ASP366 3.0 82.7 1.0 CG G:ASP98 3.4 65.2 1.0 C C:ASN364 3.4 59.7 1.0 C G:LYS94 3.6 67.7 1.0 OD2 G:ASP98 3.7 64.7 1.0 C G:GLY96 3.7 64.7 1.0 CG C:ASP366 3.7 80.3 1.0 OD1 C:ASP366 3.8 85.2 1.0 N G:GLY96 3.9 64.9 1.0 CA C:ALA365 4.1 58.2 1.0 N G:LYS94 4.1 69.0 1.0 N C:ALA365 4.2 58.2 1.0 C G:GLY95 4.3 66.6 1.0 CA G:GLY96 4.3 64.5 1.0 C C:ALA365 4.4 59.6 1.0 CA C:ASN364 4.4 59.9 1.0 N G:ASP98 4.5 65.5 1.0 CA G:LYS94 4.5 68.8 1.0 N G:GLY95 4.6 68.0 1.0 CA G:GLY95 4.6 67.3 1.0 CB G:ASP98 4.6 65.4 1.0 CB C:ASN364 4.7 60.7 1.0 N C:ASP366 4.7 62.6 1.0 N G:LEU97 4.8 64.6 1.0 O C:ALA365 4.8 58.2 1.0 C G:LEU97 4.9 66.1 1.0 O C:HOH747 4.9 46.4 1.0 O G:GLY95 4.9 67.2 1.0 CA G:ASP98 4.9 66.4 1.0 CG2 G:THR93 4.9 68.5 1.0 CB C:ASP366 5.0 73.0 1.0

Sodium binding site 4 out of 4 in the Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 4 of Murine Norovirus Protruding Domain (CW3 Strain) in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na604 b:37.5 occ:1.00 O H:LYS94 2.3 53.0 1.0 O D:ASN364 2.3 41.5 1.0 O H:GLY96 2.3 47.5 1.0 O H:HOH511 2.4 54.0 1.0 OD1 H:ASP98 2.5 45.0 1.0 OD2 D:ASP366 3.2 67.8 1.0 C D:ASN364 3.3 41.0 1.0 CG H:ASP98 3.4 44.6 1.0 C H:GLY96 3.5 47.3 1.0 C H:LYS94 3.5 52.2 1.0 N H:GLY96 3.7 49.1 1.0 CG D:ASP366 3.8 64.9 1.0 OD1 D:ASP366 3.9 69.1 1.0 OD2 H:ASP98 3.9 45.0 1.0 N H:LYS94 4.1 51.6 1.0 N H:ASP98 4.1 46.7 1.0 N D:ALA365 4.1 40.2 1.0 CA H:GLY96 4.1 48.0 1.0 CA D:ALA365 4.2 41.2 1.0 C H:GLY95 4.2 50.5 1.0 CA D:ASN364 4.3 41.6 1.0 CA H:LYS94 4.4 52.6 1.0 N H:GLY95 4.4 51.9 1.0 CA H:GLY95 4.4 51.6 1.0 CB H:ASP98 4.4 44.2 1.0 C D:ALA365 4.5 43.9 1.0 N H:LEU97 4.5 46.5 1.0 C H:LEU97 4.5 46.4 1.0 CB D:ASN364 4.5 39.8 1.0 CA H:ASP98 4.5 45.4 1.0 CA H:LEU97 4.7 42.4 1.0 N D:ASP366 4.8 46.4 1.0 O D:ALA365 5.0 42.3 1.0 O H:GLY95 5.0 51.1 1.0

T.Kilic, A.Koromyslova, V.Malak, G.S.Hansman. Crystal Structures of Murine Norovirus Protruding Domain with Conjugated Bile Acid Reveal A Novel Binding Pocket. To Be Published.