Chlorine in PDB 6c6q: Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor

The structure of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor, PDB code: 6c6q was solved by C.A.Nelson, D.H.Fremont, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	62.00 / 2.00
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	48.712, 135.245, 139.516, 90.00, 90.00, 90.00
R / Rfree (%)	18.2 / 22.2

The structure of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor also contains other interesting chemical elements:

Magnesium

(Mg)

6 atoms

The binding sites of Chlorine atom in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor (pdb code 6c6q). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 2 binding sites of Chlorine where determined in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor, PDB code: 6c6q:
Jump to Chlorine binding site number: 1; 2;

Chlorine binding site 1 out of 2 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl608 b:33.9 occ:1.00 HE A:ARG392 2.1 24.5 1.0 O A:HOH848 2.7 27.8 1.0 HH21 A:ARG392 3.0 24.0 1.0 NE A:ARG392 3.0 20.4 1.0 O B:HOH762 3.2 23.9 1.0 HB3 A:ARG392 3.2 28.6 1.0 HH11 B:ARG437 3.3 24.6 1.0 HB1 B:ALA247 3.3 28.4 1.0 O B:HOH874 3.3 34.1 1.0 HH B:TYR250 3.4 24.6 1.0 HO1 B:EDO602 3.5 43.3 1.0 HH12 B:ARG437 3.5 24.6 1.0 HB2 B:ALA247 3.5 28.4 1.0 NH2 A:ARG392 3.6 20.0 1.0 NH1 B:ARG437 3.7 20.5 1.0 CZ A:ARG392 3.8 22.7 1.0 HD3 A:ARG392 3.8 26.5 1.0 CB B:ALA247 3.9 23.7 1.0 HD2 B:PRO248 3.9 26.6 1.0 CD A:ARG392 3.9 22.1 1.0 CB A:ARG392 4.0 23.8 1.0 H11 B:EDO602 4.1 39.0 1.0 HG3 B:ARG437 4.1 28.9 1.0 HE2 B:TYR250 4.2 20.6 1.0 HB2 A:ARG392 4.2 28.6 1.0 OH B:TYR250 4.2 20.5 1.0 O1 B:EDO602 4.2 36.1 1.0 HD3 B:PRO248 4.3 26.6 1.0 HG11 A:VAL394 4.3 28.3 1.0 HG13 A:VAL394 4.4 28.3 1.0 HH22 A:ARG392 4.4 24.0 1.0 HE1 B:TRP245 4.4 19.9 1.0 CG A:ARG392 4.5 24.1 1.0 O B:TYR435 4.5 21.5 1.0 HB3 B:ALA247 4.5 28.4 1.0 CD B:PRO248 4.6 22.2 1.0 HA B:ALA247 4.6 22.8 1.0 C1 B:EDO602 4.6 32.5 1.0 HG2 A:ARG392 4.6 28.9 1.0 CG1 A:VAL394 4.8 23.6 1.0 HD2 A:ARG392 4.8 26.5 1.0 HD3 B:ARG437 4.8 27.3 1.0 O A:ARG392 4.9 23.2 1.0 H21 B:EDO602 4.9 33.6 1.0 CA B:ALA247 4.9 19.0 1.0 CZ B:ARG437 4.9 23.3 1.0 H22 B:EDO602 4.9 33.6 1.0 CG B:ARG437 4.9 24.1 1.0 CE2 B:TYR250 4.9 17.2 1.0 O A:HOH703 5.0 22.2 1.0

Chlorine binding site 2 out of 2 in the Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of Crystal Structure of the Murine Norovirus VP1 P Domain in Complex with the CD300LF Receptor within 5.0Å range: probe atom residue distance (Å) B Occ A:Cl609 b:32.0 occ:1.00 HE B:ARG392 2.1 25.5 1.0 O B:HOH780 2.9 24.5 1.0 O A:HOH890 3.0 33.5 1.0 NE B:ARG392 3.0 21.2 1.0 O A:HOH787 3.0 18.6 1.0 HH11 A:ARG437 3.1 26.7 1.0 HH21 B:ARG392 3.1 31.6 1.0 HB3 B:ARG392 3.2 29.3 1.0 HH12 A:ARG437 3.3 26.7 1.0 HB1 A:ALA247 3.5 26.2 1.0 NH1 A:ARG437 3.5 22.2 1.0 HB2 A:ALA247 3.6 26.2 1.0 NH2 B:ARG392 3.7 26.3 1.0 HD3 B:ARG392 3.7 28.5 1.0 CZ B:ARG392 3.8 20.8 1.0 CD B:ARG392 3.9 23.8 1.0 HG3 A:ARG437 4.0 24.6 1.0 CB A:ALA247 4.0 21.9 1.0 CB B:ARG392 4.1 24.4 1.0 HG11 B:VAL394 4.1 25.1 1.0 HD2 A:PRO248 4.1 20.3 1.0 HG13 B:VAL394 4.2 25.1 1.0 HB2 B:ARG392 4.3 29.3 1.0 CG B:ARG392 4.4 27.8 1.0 HG2 B:ARG392 4.4 33.4 1.0 HE2 A:TYR250 4.5 23.9 1.0 OH A:TYR250 4.5 28.0 1.0 HE1 A:TRP245 4.5 24.8 1.0 HH22 B:ARG392 4.5 31.6 1.0 HD3 A:PRO248 4.5 20.3 1.0 CG1 B:VAL394 4.6 20.9 1.0 HA A:ALA247 4.6 26.4 1.0 O A:TYR435 4.6 20.9 1.0 O A:HOH771 4.7 23.6 1.0 HB3 A:ALA247 4.7 26.2 1.0 O B:ARG392 4.7 23.8 1.0 HD3 A:ARG437 4.7 23.8 1.0 HD2 B:ARG392 4.7 28.5 1.0 CZ A:ARG437 4.7 22.4 1.0 CD A:PRO248 4.8 16.9 1.0 CG A:ARG437 4.8 20.5 1.0 HG12 B:VAL394 4.9 25.1 1.0 CA A:ALA247 4.9 22.0 1.0

C.A.Nelson, C.B.Wilen, Y.N.Dai, R.C.Orchard, A.S.Kim, R.A.Stegeman, L.L.Hsieh, T.J.Smith, H.W.Virgin, D.H.Fremont. Structural Basis For Murine Norovirus Engagement of Bile Acids and the CD300LF Receptor. Proc. Natl. Acad. Sci. V. 115 E9201 2018U.S.A..
ISSN: ESSN 1091-6490
PubMed: 30194229
DOI: 10.1073/PNAS.1805797115