Sodium in PDB 6h6m: CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca)

The structure of CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca), PDB code: 6h6m 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)	46.66 / 2.38
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	75.940, 137.550, 93.800, 90.00, 95.84, 90.00
R / Rfree (%)	18.6 / 22.5

The binding sites of Sodium atom in the CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) (pdb code 6h6m). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 4 binding sites of Sodium where determined in the CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca), PDB code: 6h6m:
Jump to Sodium binding site number: 1; 2; 3; 4;

Sodium binding site 1 out of 4 in the CR10 Murine Norovirus Protruding Domain 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 CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ A:Na606 b:36.5 occ:1.00 O A:ASN364 2.3 37.2 1.0 O E:GLY96 2.4 35.8 1.0 OD1 E:ASP98 2.4 39.3 1.0 O E:LYS94 2.4 42.8 1.0 O E:HOH316 2.5 34.4 1.0 CG E:ASP98 3.2 37.4 1.0 C A:ASN364 3.4 35.9 1.0 C E:GLY96 3.5 35.8 1.0 C E:LYS94 3.5 44.7 1.0 OD2 E:ASP98 3.6 37.7 1.0 OD2 A:ASP366 3.7 40.2 1.0 N E:GLY96 3.7 39.1 1.0 CA A:VAL365 4.0 34.1 1.0 N E:LYS94 4.0 44.5 1.0 N A:VAL365 4.1 34.4 1.0 N E:ASP98 4.1 36.0 1.0 CA E:GLY96 4.2 36.7 1.0 C E:GLY95 4.2 42.0 1.0 O A:HOH706 4.2 44.8 1.0 CB E:ASP98 4.3 35.8 1.0 CA E:LYS94 4.3 46.1 1.0 N E:GLY95 4.4 45.2 1.0 CA E:GLY95 4.4 43.9 1.0 C A:VAL365 4.4 33.3 1.0 C E:LEU97 4.5 36.6 1.0 CA A:ASN364 4.5 36.3 1.0 N E:LEU97 4.5 35.0 1.0 CA E:ASP98 4.5 36.6 1.0 CG A:ASP366 4.6 39.5 1.0 CB A:ASN364 4.7 38.2 1.0 O A:VAL365 4.7 32.5 1.0 CA E:LEU97 4.7 34.4 1.0 O E:GLY95 4.9 42.7 1.0 CB E:LYS94 4.9 47.2 1.0

Sodium binding site 2 out of 4 in the CR10 Murine Norovirus Protruding Domain 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 CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ B:Na601 b:45.1 occ:1.00 O B:HOH800 2.7 53.7 1.0 O B:HOH769 2.7 42.5 1.0 OE1 B:GLN438 2.7 35.2 1.0 OD2 B:ASP440 2.7 35.9 1.0 OE2 B:GLU447 2.8 41.0 1.0 CD B:GLU447 3.7 38.4 1.0 CD B:GLN438 3.8 33.5 1.0 CG B:ASP440 3.9 36.3 1.0 OE1 B:GLU447 4.1 39.6 1.0 NE2 B:GLN438 4.2 31.4 1.0 O B:HOH738 4.3 31.1 1.0 O B:HOH777 4.4 27.1 1.0 CB B:ASP440 4.4 35.4 1.0 O B:ALA445 4.7 36.7 1.0 CG B:GLU447 4.9 34.9 1.0 CB B:ASP443 4.9 49.6 1.0 OD1 B:ASP440 4.9 37.2 1.0 CB B:GLU447 4.9 31.9 1.0

Sodium binding site 3 out of 4 in the CR10 Murine Norovirus Protruding Domain 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 CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ C:Na605 b:42.1 occ:1.00 O C:ASN364 2.3 32.0 1.0 OD1 F:ASP98 2.4 35.5 1.0 O F:GLY96 2.4 36.8 1.0 O F:LYS94 2.4 36.8 1.0 O C:HOH811 2.8 37.3 1.0 CG F:ASP98 3.2 35.3 1.0 C C:ASN364 3.5 32.7 1.0 C F:GLY96 3.5 37.2 1.0 OD2 F:ASP98 3.5 34.4 1.0 C F:LYS94 3.5 36.6 1.0 OD2 C:ASP366 3.6 38.1 1.0 N F:GLY96 3.8 37.5 1.0 N F:LYS94 4.0 32.8 1.0 O F:HOH336 4.0 38.6 1.0 N F:ASP98 4.1 36.2 1.0 CA F:GLY96 4.2 37.7 1.0 CA C:VAL365 4.2 33.2 1.0 N C:VAL365 4.2 33.3 1.0 C F:GLY95 4.2 38.4 1.0 O F:HOH301 4.3 25.5 1.0 CB F:ASP98 4.3 34.0 1.0 CA F:LYS94 4.4 34.2 1.0 C F:LEU97 4.5 35.2 1.0 N F:GLY95 4.5 38.1 1.0 CA F:GLY95 4.5 37.8 1.0 N F:LEU97 4.5 33.3 1.0 CA C:ASN364 4.5 33.3 1.0 CA F:ASP98 4.5 35.3 1.0 CB C:ASN364 4.6 35.4 1.0 C C:VAL365 4.6 31.6 1.0 CG C:ASP366 4.7 37.4 1.0 CG F:LYS94 4.7 31.5 1.0 CA F:LEU97 4.7 35.6 1.0 O F:GLY95 4.9 39.5 1.0 O C:VAL365 4.9 29.4 1.0 O F:LEU97 5.0 33.4 1.0

Sodium binding site 4 out of 4 in the CR10 Murine Norovirus Protruding Domain 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 CR10 Murine Norovirus Protruding Domain in Complex with the CD300LF Receptor and Glycochenodeoxycholate (Gcdca) within 5.0Å range: probe atom residue distance (Å) B Occ D:Na601 b:44.0 occ:1.00 O D:HOH764 2.4 45.3 1.0 O D:HOH707 2.5 29.1 1.0 OD2 D:ASP440 2.5 44.1 1.0 OE1 D:GLN438 2.5 38.5 1.0 O D:HOH769 2.8 54.5 1.0 OE2 D:GLU447 2.8 50.0 1.0 CG D:ASP440 3.5 43.8 1.0 CD D:GLN438 3.7 36.5 1.0 CB D:ASP440 4.0 41.8 1.0 CD D:GLU447 4.1 47.9 1.0 O D:HOH730 4.2 29.6 1.0 NE2 D:GLN438 4.2 35.5 1.0 CB D:ASP443 4.3 51.5 1.0 O D:ALA445 4.4 36.4 1.0 O D:ASP443 4.4 48.0 1.0 OD1 D:ASP440 4.5 45.5 1.0 O D:HOH779 4.6 25.9 1.0 OD2 D:ASP443 4.6 56.0 1.0 CG D:ASP443 4.7 55.2 1.0 OE1 D:GLU447 4.8 47.9 1.0 CG D:GLN438 4.9 34.7 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.