Fluorine in PDB 4y2d: Crystal Structure of the MCD1D/7DW8-5/Inktcr Ternary Complex

The structure of Crystal Structure of the MCD1D/7DW8-5/Inktcr Ternary Complex, PDB code: 4y2d was solved by D.M.Zajonc, E.D.Yu, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.41 / 3.05
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	79.422, 150.264, 100.800, 90.00, 96.24, 90.00
R / Rfree (%)	21.7 / 25.7

The binding sites of Fluorine atom in the Crystal Structure of the MCD1D/7DW8-5/Inktcr Ternary Complex (pdb code 4y2d). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of the MCD1D/7DW8-5/Inktcr Ternary Complex, PDB code: 4y2d:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in the Crystal Structure of the MCD1D/7DW8-5/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/7DW8-5/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:60.7 occ:0.50 F1 A:7DW304 0.0 60.7 0.5 CBF A:7DW304 1.4 59.2 0.5 CBA A:7DW304 2.4 59.4 0.5 CBE A:7DW304 2.4 57.6 0.5 CD1 A:ILE47 3.1 68.0 1.0 CG1 A:ILE47 3.5 68.0 1.0 CE3 A:TRP40 3.5 58.9 1.0 CBB A:7DW304 3.6 58.0 0.5 CBD A:7DW304 3.7 56.1 0.5 CBC A:7DW304 4.1 56.2 0.5 CZ3 A:TRP40 4.2 58.1 1.0 CD2 A:TRP40 4.5 60.3 1.0 CG A:PHE70 4.5 66.7 1.0 CG2 A:ILE47 4.5 70.5 1.0 CB A:TRP40 4.5 61.6 1.0 CB A:ILE47 4.6 69.9 1.0 CD1 A:PHE70 4.7 65.5 1.0 CD2 A:PHE70 4.7 68.8 1.0 CG2 A:VAL30 4.8 63.0 1.0 CB A:SER28 4.8 57.4 1.0 CB A:PHE70 4.9 66.6 1.0 CG A:TRP40 4.9 61.5 1.0 CE1 A:PHE70 5.0 65.5 1.0 CE2 A:PHE70 5.0 69.3 1.0

Fluorine binding site 2 out of 4 in the Crystal Structure of the MCD1D/7DW8-5/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/7DW8-5/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ A:F304 b:62.8 occ:0.50 F1 A:7DW304 0.0 62.8 0.5 CBF A:7DW304 1.3 60.6 0.5 CBA A:7DW304 2.3 60.3 0.5 CBE A:7DW304 2.3 58.9 0.5 CBB A:7DW304 3.6 58.1 0.5 CBD A:7DW304 3.6 56.8 0.5 CD2 A:PHE171 3.6 71.5 1.0 CG2 A:THR167 3.8 71.2 1.0 CB A:PHE171 4.0 74.9 1.0 CA A:CYS168 4.0 72.4 1.0 CBC A:7DW304 4.1 56.4 0.5 CG A:PHE171 4.1 74.1 1.0 CD2 A:LEU66 4.2 77.6 1.0 N A:CYS168 4.2 71.9 1.0 O A:THR167 4.3 75.4 1.0 C A:THR167 4.3 73.3 1.0 CE2 A:PHE171 4.4 71.3 1.0 CB A:THR167 4.6 70.6 1.0 CB A:CYS168 4.7 71.0 1.0 CE2 A:PHE10 4.7 67.0 1.0 CD1 A:LEU66 4.9 74.3 1.0

Fluorine binding site 3 out of 4 in the Crystal Structure of the MCD1D/7DW8-5/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/7DW8-5/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F506 b:61.5 occ:0.50 F1 E:7DW506 0.0 61.5 0.5 CBF E:7DW506 1.3 60.0 0.5 CBA E:7DW506 2.4 59.7 0.5 CBE E:7DW506 2.4 59.1 0.5 CBB E:7DW506 3.6 58.2 0.5 CBD E:7DW506 3.6 57.6 0.5 CG2 E:VAL30 3.8 67.5 1.0 CD1 E:ILE47 4.0 63.8 1.0 CBC E:7DW506 4.1 57.0 0.5 CG1 E:ILE47 4.4 64.7 1.0 CG2 E:ILE47 4.6 68.9 1.0 CD2 E:PHE70 4.8 69.7 1.0 CE2 E:PHE70 4.8 70.5 1.0 CG E:PHE70 4.9 67.5 1.0 CE3 E:TRP40 4.9 61.7 1.0 SG E:CYS12 5.0 68.8 1.0 CZ E:PHE70 5.0 69.0 1.0

Fluorine binding site 4 out of 4 in the Crystal Structure of the MCD1D/7DW8-5/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/7DW8-5/Inktcr Ternary Complex within 5.0Å range: probe atom residue distance (Å) B Occ E:F506 b:61.7 occ:0.50 F1 E:7DW506 0.0 61.7 0.5 CBF E:7DW506 1.3 59.6 0.5 CBA E:7DW506 2.3 58.8 0.5 CBE E:7DW506 2.3 58.6 0.5 O E:THR167 3.5 74.4 1.0 CBB E:7DW506 3.6 56.9 0.5 CBD E:7DW506 3.6 56.9 0.5 CD2 E:PHE171 3.8 77.9 1.0 CG2 E:THR167 3.9 70.2 1.0 C E:THR167 3.9 73.1 1.0 CBC E:7DW506 4.0 56.0 0.5 CA E:CYS168 4.1 73.8 1.0 CB E:PHE171 4.1 79.8 1.0 N E:CYS168 4.2 72.6 1.0 CD2 E:LEU66 4.2 72.2 1.0 CG E:PHE171 4.3 79.8 1.0 CB E:THR167 4.5 69.7 1.0 CE2 E:PHE171 4.6 78.1 1.0 CD1 E:LEU66 4.7 68.2 1.0 CB E:CYS168 4.8 72.5 1.0 CA E:THR167 4.9 72.7 1.0 CE2 E:PHE10 4.9 73.4 1.0

A.Birkholz, M.Nemcovic, E.D.Yu, E.Girardi, J.Wang, A.Khurana, N.Pauwels, R.W.Franck, M.Tsuji, A.Howell, S.Calenbergh, M.Kronenberg, D.M.Zajonc. Structural Modifications of Alphagalcer in Both Lipid and Carbohydrate Moiety Influence Activation of Murine and Human Inkt Cells To Be Published.