Fluorine in PDB 6mjq: Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex, PDB code: 6mjq was solved by D.M.Zajonc, A.Bitra, J.Janssens, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.75 / 3.00
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	78.967, 191.858, 150.957, 90.00, 90.02, 90.00
R / Rfree (%)	21.5 / 25.8

The structure of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex also contains other interesting chemical elements:

Sodium

(Na)

3 atoms

The binding sites of Fluorine atom in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex (pdb code 6mjq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex, PDB code: 6mjq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F308 b:75.5 occ:1.00 FBS A:JUD308 0.0 75.5 1.0 CBA A:JUD308 1.4 74.9 1.0 FBT A:JUD308 2.2 76.3 1.0 FBR A:JUD308 2.2 76.1 1.0 CAX A:JUD308 2.3 72.4 1.0 CAW A:JUD308 2.7 70.6 1.0 CAY A:JUD308 3.5 70.8 1.0 CA A:GLY155 3.9 44.2 1.0 CAV A:JUD308 4.1 69.6 1.0 CB A:ALA158 4.2 41.4 1.0 N A:GLY155 4.4 44.5 1.0 O A:GLN154 4.5 44.9 1.0 CAZ A:JUD308 4.7 69.4 1.0 C A:GLN154 4.7 45.0 1.0 O A:GLY155 4.9 44.3 1.0 CAU A:JUD308 4.9 68.0 1.0 C A:GLY155 4.9 44.0 1.0

Fluorine binding site 2 out of 6 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F308 b:76.3 occ:1.00 FBT A:JUD308 0.0 76.3 1.0 CBA A:JUD308 1.4 74.9 1.0 FBS A:JUD308 2.2 75.5 1.0 FBR A:JUD308 2.2 76.1 1.0 CAX A:JUD308 2.3 72.4 1.0 CAW A:JUD308 3.1 70.6 1.0 CAY A:JUD308 3.1 70.8 1.0 OD1 C:ASP52 3.6 61.3 1.0 O C:HOH413 3.6 30.0 1.0 O C:VAL51 4.3 54.2 1.0 CAV A:JUD308 4.3 69.6 1.0 CAZ A:JUD308 4.3 69.4 1.0 CA C:ASP52 4.5 57.9 1.0 CG C:ASP52 4.7 60.5 1.0 C C:VAL51 4.7 53.9 1.0 N C:ASP52 4.8 56.0 1.0 CAU A:JUD308 4.9 68.0 1.0

Fluorine binding site 3 out of 6 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F308 b:76.1 occ:1.00 FBR A:JUD308 0.0 76.1 1.0 CBA A:JUD308 1.4 74.9 1.0 FBT A:JUD308 2.2 76.3 1.0 FBS A:JUD308 2.2 75.5 1.0 CAX A:JUD308 2.3 72.4 1.0 CAY A:JUD308 2.7 70.8 1.0 CAW A:JUD308 3.6 70.6 1.0 CAZ A:JUD308 4.1 69.4 1.0 CA A:GLY155 4.1 44.2 1.0 N A:GLY155 4.2 44.5 1.0 CAV A:JUD308 4.7 69.6 1.0 C A:GLN154 4.7 45.0 1.0 CB A:GLN154 4.7 47.1 1.0 CAU A:JUD308 4.9 68.0 1.0 CB C:VAL51 5.0 52.1 1.0

Fluorine binding site 4 out of 6 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F311 b:70.2 occ:1.00 FBS E:JUD311 0.0 70.2 1.0 CBA E:JUD311 1.4 69.7 1.0 FBT E:JUD311 2.2 70.9 1.0 FBR E:JUD311 2.2 71.3 1.0 CAX E:JUD311 2.3 67.6 1.0 CAW E:JUD311 2.7 66.3 1.0 CAY E:JUD311 3.5 65.9 1.0 CB E:ALA158 3.6 41.5 1.0 CA E:GLY155 3.8 42.6 1.0 CAV E:JUD311 4.1 65.3 1.0 O E:GLN154 4.4 42.9 1.0 O E:GLY155 4.5 42.8 1.0 N E:GLY155 4.5 42.9 1.0 CAZ E:JUD311 4.6 64.8 1.0 C E:GLY155 4.7 42.5 1.0 C E:GLN154 4.7 43.1 1.0 CAU E:JUD311 4.9 63.6 1.0

Fluorine binding site 5 out of 6 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F311 b:70.9 occ:1.00 FBT E:JUD311 0.0 70.9 1.0 CBA E:JUD311 1.4 69.7 1.0 FBS E:JUD311 2.2 70.2 1.0 FBR E:JUD311 2.2 71.3 1.0 CAX E:JUD311 2.3 67.6 1.0 CAW E:JUD311 3.0 66.3 1.0 CAY E:JUD311 3.2 65.9 1.0 OD1 G:ASP52 4.0 59.3 1.0 CAV E:JUD311 4.3 65.3 1.0 CAZ E:JUD311 4.4 64.8 1.0 CAU E:JUD311 4.9 63.6 1.0 O G:VAL51 4.9 52.2 1.0 CA G:ASP52 5.0 55.6 1.0

Fluorine binding site 6 out of 6 in the Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Crystal Structure of the MCD1D/Xxp (JJ295) /Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F311 b:71.3 occ:1.00 FBR E:JUD311 0.0 71.3 1.0 CBA E:JUD311 1.4 69.7 1.0 FBS E:JUD311 2.2 70.2 1.0 FBT E:JUD311 2.2 70.9 1.0 CAX E:JUD311 2.3 67.6 1.0 CAY E:JUD311 2.7 65.9 1.0 CAW E:JUD311 3.6 66.3 1.0 CA E:GLY155 4.0 42.6 1.0 CAZ E:JUD311 4.1 64.8 1.0 N E:GLY155 4.2 42.9 1.0 C E:GLN154 4.6 43.1 1.0 CAV E:JUD311 4.7 65.3 1.0 CB E:GLN154 4.8 44.5 1.0 O E:GLN154 4.9 42.9 1.0 CAU E:JUD311 4.9 63.6 1.0

J.Janssens, A.Bitra, J.Wang, T.Decruy, K.Venken, J.Van Der Eycken, D.Elewaut, D.M.Zajonc, S.Van Calenbergh. 4"-O-Alkylated Alpha-Galactosylceramide Analogues As Inkt-Cell Antigens: Synthetic, Biological, and Structural Studies. Chemmedchem V. 14 147 2019.
ISSN: ESSN 1860-7187
PubMed: 30556652
DOI: 10.1002/CMDC.201800649